Starting phenix.real_space_refine on Mon May 26 08:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hga_52132/05_2025/9hga_52132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hga_52132/05_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_52132/05_2025/9hga_52132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hga_52132/05_2025/9hga_52132.map" model { file = "/net/cci-nas-00/data/ceres_data/9hga_52132/05_2025/9hga_52132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hga_52132/05_2025/9hga_52132.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.39, per 1000 atoms: 0.48 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: 7.89 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.32 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: 10.61 Time building geometry restraints manager: 9.27 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.490 Extract box with map and model: 1.200 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 59.840 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.430 ------------------------------------------------------------------------------- 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 : 5.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (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 TRP 0.009 0.001 TRP A 546 HIS 0.002 0.000 HIS F 266 PHE 0.009 0.001 PHE A 72 TYR 0.009 0.001 TYR D 184 ARG 0.001 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.19694 ( 619) hydrogen bonds : angle 7.26553 ( 1752) SS BOND : bond 0.00224 ( 1) SS BOND : angle 1.22703 ( 2) covalent geometry : bond 0.00245 (14499) covalent geometry : angle 0.44363 (19680) 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 : 2.218 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: 0.9199 (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: 0.5268 time to fit residues: 90.5791 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 : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.096599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065535 restraints weight = 130222.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068045 restraints weight = 48000.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.069557 restraints weight = 26876.453| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14502 Z= 0.188 Angle : 0.495 6.924 19682 Z= 0.270 Chirality : 0.042 0.149 2155 Planarity : 0.003 0.035 2602 Dihedral : 3.483 17.337 1987 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.20 % Allowed : 10.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1797 helix: 2.33 (0.23), residues: 516 sheet: 0.28 (0.23), residues: 495 loop : -0.65 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 776 HIS 0.003 0.001 HIS B 165 PHE 0.007 0.001 PHE A 517 TYR 0.008 0.001 TYR D 184 ARG 0.003 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 619) hydrogen bonds : angle 5.58151 ( 1752) SS BOND : bond 0.00376 ( 1) SS BOND : angle 1.35175 ( 2) covalent geometry : bond 0.00388 (14499) covalent geometry : angle 0.49517 (19680) Misc. bond : bond 0.00199 ( 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 111 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 2.319 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: C 41 TYR cc_start: 0.7466 (p90) cc_final: 0.7159 (p90) REVERT: D 187 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8548 (tm-30) REVERT: E 50 MET cc_start: 0.8296 (mmp) cc_final: 0.8045 (mmp) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.5739 time to fit residues: 97.9161 Evaluate side-chains 107 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 2.410 ------------------------------------------------------------------------------- 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 85 optimal weight: 7.9990 chunk 17 optimal weight: 0.1980 chunk 111 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 chunk 177 optimal weight: 8.9990 chunk 173 optimal weight: 50.0000 chunk 158 optimal weight: 20.0000 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.093039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.062124 restraints weight = 133978.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064414 restraints weight = 51168.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065860 restraints weight = 29435.206| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 14502 Z= 0.372 Angle : 0.622 7.279 19682 Z= 0.340 Chirality : 0.044 0.179 2155 Planarity : 0.004 0.054 2602 Dihedral : 4.193 17.736 1987 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.44 % Allowed : 12.21 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 1797 helix: 1.44 (0.22), residues: 509 sheet: -0.15 (0.23), residues: 487 loop : -1.18 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.005 0.002 HIS D 102 PHE 0.013 0.002 PHE A 517 TYR 0.017 0.002 TYR D 205 ARG 0.004 0.001 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 619) hydrogen bonds : angle 5.79119 ( 1752) SS BOND : bond 0.00593 ( 1) SS BOND : angle 1.81196 ( 2) covalent geometry : bond 0.00772 (14499) covalent geometry : angle 0.62223 (19680) Misc. bond : bond 0.00146 ( 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 124 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 2.113 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: A 403 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: A 777 MET cc_start: 0.9362 (tpt) cc_final: 0.9019 (tpt) REVERT: D 187 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8430 (tm-30) outliers start: 22 outliers final: 13 residues processed: 120 average time/residue: 0.5252 time to fit residues: 96.1488 Evaluate side-chains 111 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 622 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 64 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.104315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073416 restraints weight = 129241.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076006 restraints weight = 47781.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.077648 restraints weight = 26728.828| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14502 Z= 0.107 Angle : 0.471 6.090 19682 Z= 0.252 Chirality : 0.042 0.151 2155 Planarity : 0.003 0.051 2602 Dihedral : 3.861 18.376 1987 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.66 % Allowed : 12.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1797 helix: 2.09 (0.23), residues: 502 sheet: -0.03 (0.23), residues: 490 loop : -0.87 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.004 0.001 HIS B 64 PHE 0.008 0.001 PHE E 74 TYR 0.011 0.001 TYR D 184 ARG 0.002 0.000 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 619) hydrogen bonds : angle 5.15515 ( 1752) SS BOND : bond 0.00000 ( 1) SS BOND : angle 1.03198 ( 2) covalent geometry : bond 0.00228 (14499) covalent geometry : angle 0.47060 (19680) Misc. bond : bond 0.00056 ( 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 117 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 116 average time/residue: 0.5330 time to fit residues: 94.3904 Evaluate side-chains 109 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 147 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3724 r_free = 0.3724 target = 0.103442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072327 restraints weight = 129669.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074915 restraints weight = 48190.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076554 restraints weight = 27079.204| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14502 Z= 0.170 Angle : 0.476 5.996 19682 Z= 0.257 Chirality : 0.041 0.138 2155 Planarity : 0.003 0.043 2602 Dihedral : 3.821 17.490 1987 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.79 % Allowed : 13.39 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1797 helix: 2.13 (0.23), residues: 502 sheet: -0.20 (0.23), residues: 492 loop : -0.82 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 348 HIS 0.003 0.001 HIS B 64 PHE 0.008 0.001 PHE A 72 TYR 0.011 0.001 TYR D 184 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 619) hydrogen bonds : angle 5.11441 ( 1752) SS BOND : bond 0.00218 ( 1) SS BOND : angle 1.14842 ( 2) covalent geometry : bond 0.00359 (14499) covalent geometry : angle 0.47629 (19680) Misc. bond : bond 0.00042 ( 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 111 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 2.453 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 403 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7814 (mp10) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.5576 time to fit residues: 92.9429 Evaluate side-chains 108 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.102485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071179 restraints weight = 131589.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073741 restraints weight = 49148.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075378 restraints weight = 27771.319| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14502 Z= 0.218 Angle : 0.502 5.438 19682 Z= 0.272 Chirality : 0.041 0.142 2155 Planarity : 0.003 0.051 2602 Dihedral : 3.940 16.957 1987 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.25 % Allowed : 13.53 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1797 helix: 2.03 (0.23), residues: 498 sheet: -0.31 (0.23), residues: 491 loop : -0.93 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 776 HIS 0.003 0.001 HIS B 165 PHE 0.010 0.001 PHE A 72 TYR 0.010 0.001 TYR D 184 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 619) hydrogen bonds : angle 5.14565 ( 1752) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.30030 ( 2) covalent geometry : bond 0.00457 (14499) covalent geometry : angle 0.50223 (19680) Misc. bond : bond 0.00072 ( 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 123 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 2.354 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: A 403 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7902 (mp10) outliers start: 19 outliers final: 14 residues processed: 121 average time/residue: 0.5304 time to fit residues: 97.5638 Evaluate side-chains 116 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 VAL 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 99 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** D 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.103828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072799 restraints weight = 130109.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075399 restraints weight = 48004.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077051 restraints weight = 26909.349| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14502 Z= 0.105 Angle : 0.461 5.172 19682 Z= 0.246 Chirality : 0.042 0.139 2155 Planarity : 0.003 0.047 2602 Dihedral : 3.809 17.204 1987 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.05 % Allowed : 13.66 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1797 helix: 2.29 (0.23), residues: 499 sheet: -0.22 (0.23), residues: 489 loop : -0.76 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.003 0.001 HIS B 64 PHE 0.007 0.001 PHE A 72 TYR 0.012 0.001 TYR D 184 ARG 0.004 0.000 ARG F 418 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 619) hydrogen bonds : angle 4.88406 ( 1752) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.25593 ( 2) covalent geometry : bond 0.00228 (14499) covalent geometry : angle 0.46125 (19680) Misc. bond : bond 0.00047 ( 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 120 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 2.515 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: A 403 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7812 (mp10) outliers start: 16 outliers final: 13 residues processed: 118 average time/residue: 0.5536 time to fit residues: 99.9633 Evaluate side-chains 116 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 283 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.103207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.072094 restraints weight = 130455.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.074674 restraints weight = 48477.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076328 restraints weight = 27326.956| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1970 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= 0.146 Angle : 0.468 4.962 19682 Z= 0.250 Chirality : 0.041 0.136 2155 Planarity : 0.003 0.045 2602 Dihedral : 3.795 16.585 1987 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.92 % Allowed : 13.99 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1797 helix: 2.24 (0.23), residues: 493 sheet: -0.24 (0.23), residues: 482 loop : -0.79 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 348 HIS 0.003 0.001 HIS B 64 PHE 0.007 0.001 PHE A 72 TYR 0.011 0.001 TYR D 184 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 619) hydrogen bonds : angle 4.92555 ( 1752) SS BOND : bond 0.00297 ( 1) SS BOND : angle 1.22053 ( 2) covalent geometry : bond 0.00310 (14499) covalent geometry : angle 0.46833 (19680) Misc. bond : bond 0.00029 ( 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 117 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 2.166 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: 0.8147 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: D 56 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8567 (mt-10) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.5355 time to fit residues: 93.7219 Evaluate side-chains 116 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR 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 615 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 283 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 33 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 174 optimal weight: 30.0000 chunk 135 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.070839 restraints weight = 131456.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.073396 restraints weight = 49646.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075029 restraints weight = 28153.866| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14502 Z= 0.222 Angle : 0.512 5.428 19682 Z= 0.276 Chirality : 0.041 0.133 2155 Planarity : 0.003 0.048 2602 Dihedral : 3.941 15.684 1987 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.18 % Allowed : 14.12 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1797 helix: 2.00 (0.23), residues: 496 sheet: -0.34 (0.23), residues: 480 loop : -0.93 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 776 HIS 0.003 0.001 HIS B 64 PHE 0.009 0.001 PHE A 72 TYR 0.011 0.001 TYR D 184 ARG 0.003 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 619) hydrogen bonds : angle 5.09610 ( 1752) SS BOND : bond 0.00395 ( 1) SS BOND : angle 1.39358 ( 2) covalent geometry : bond 0.00467 (14499) covalent geometry : angle 0.51155 (19680) Misc. bond : bond 0.00070 ( 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: 18 poor density : 100 time to evaluate : 2.192 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: A 403 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8079 (mp10) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.5335 time to fit residues: 94.3388 Evaluate side-chains 114 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR 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 615 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.102535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071444 restraints weight = 130601.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074027 restraints weight = 48680.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075656 restraints weight = 27495.762| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14502 Z= 0.166 Angle : 0.486 5.763 19682 Z= 0.260 Chirality : 0.041 0.133 2155 Planarity : 0.003 0.050 2602 Dihedral : 3.898 15.964 1987 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.18 % Allowed : 13.85 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1797 helix: 2.09 (0.23), residues: 493 sheet: -0.30 (0.23), residues: 475 loop : -0.89 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 776 HIS 0.004 0.001 HIS B 64 PHE 0.007 0.001 PHE A 663 TYR 0.011 0.001 TYR D 184 ARG 0.003 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 619) hydrogen bonds : angle 4.98760 ( 1752) SS BOND : bond 0.00321 ( 1) SS BOND : angle 1.28673 ( 2) covalent geometry : bond 0.00350 (14499) covalent geometry : angle 0.48553 (19680) Misc. bond : bond 0.00027 ( 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 119 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 2.133 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: A 403 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: B 282 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8114 (mm-30) REVERT: D 219 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8656 (tm-30) outliers start: 18 outliers final: 16 residues processed: 117 average time/residue: 0.5355 time to fit residues: 95.9221 Evaluate side-chains 117 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR 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 467 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 283 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 0.1980 chunk 148 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.102621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071514 restraints weight = 130577.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074100 restraints weight = 48742.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.075754 restraints weight = 27520.147| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14502 Z= 0.173 Angle : 0.485 5.942 19682 Z= 0.260 Chirality : 0.041 0.134 2155 Planarity : 0.003 0.047 2602 Dihedral : 3.887 15.574 1987 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.25 % Allowed : 13.92 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1797 helix: 2.09 (0.23), residues: 493 sheet: -0.31 (0.23), residues: 475 loop : -0.91 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 546 HIS 0.004 0.001 HIS B 64 PHE 0.007 0.001 PHE A 395 TYR 0.010 0.001 TYR D 184 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 619) hydrogen bonds : angle 4.96729 ( 1752) SS BOND : bond 0.00339 ( 1) SS BOND : angle 1.30275 ( 2) covalent geometry : bond 0.00365 (14499) covalent geometry : angle 0.48465 (19680) Misc. bond : bond 0.00036 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7409.36 seconds wall clock time: 129 minutes 7.73 seconds (7747.73 seconds total)