Starting phenix.real_space_refine on Tue Jun 24 04:00:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hga_52132/06_2025/9hga_52132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hga_52132/06_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_52132/06_2025/9hga_52132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hga_52132/06_2025/9hga_52132.map" model { file = "/net/cci-nas-00/data/ceres_data/9hga_52132/06_2025/9hga_52132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hga_52132/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.47, per 1000 atoms: 0.52 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: 7.52 Conformation dependent library (CDL) restraints added in 2.4 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: 2.35 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: 13.00 Time building geometry restraints manager: 9.14 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: 3.240 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: 0.520 Extract box with map and model: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 63.890 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.130 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 73.530 ------------------------------------------------------------------------------- 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 : 2.657 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: 0.6912 time to fit residues: 120.4620 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 : 2.477 ------------------------------------------------------------------------------- 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 = 0.096608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065599 restraints weight = 129929.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068105 restraints weight = 47902.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.069614 restraints weight = 26792.902| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 5.58152 ( 1752) SS BOND : bond 0.00376 ( 1) SS BOND : angle 1.35173 ( 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 : 2.083 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: 0.7422 (p90) cc_final: 0.7122 (p90) REVERT: D 187 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8531 (tm-30) REVERT: E 50 MET cc_start: 0.8226 (mmp) cc_final: 0.7990 (mmp) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.5627 time to fit residues: 96.0792 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 : 2.091 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 chunk 173 optimal weight: 50.0000 chunk 158 optimal weight: 20.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.093864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063485 restraints weight = 134707.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065924 restraints weight = 50546.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067482 restraints weight = 28514.464| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14502 Z= 0.317 Angle : 0.570 6.218 19682 Z= 0.311 Chirality : 0.042 0.140 2155 Planarity : 0.004 0.050 2602 Dihedral : 3.966 17.648 1987 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.25 % Allowed : 11.82 % Favored : 86.93 % 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: 0.05 (0.20), residues: 1797 helix: 1.78 (0.22), residues: 508 sheet: -0.06 (0.23), residues: 480 loop : -1.03 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.005 0.001 HIS B 64 PHE 0.011 0.001 PHE D 147 TYR 0.014 0.002 TYR D 205 ARG 0.003 0.000 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 619) hydrogen bonds : angle 5.62634 ( 1752) SS BOND : bond 0.00489 ( 1) SS BOND : angle 1.67321 ( 2) covalent geometry : bond 0.00659 (14499) covalent geometry : angle 0.57020 (19680) Misc. bond : bond 0.00135 ( 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 122 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 2.297 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: 0.8115 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: D 187 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8441 (tm-30) outliers start: 19 outliers final: 12 residues processed: 118 average time/residue: 0.5369 time to fit residues: 96.7896 Evaluate side-chains 112 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 135 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.104065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072929 restraints weight = 130606.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.075520 restraints weight = 49304.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077127 restraints weight = 27904.005| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14502 Z= 0.138 Angle : 0.472 5.365 19682 Z= 0.254 Chirality : 0.042 0.140 2155 Planarity : 0.003 0.049 2602 Dihedral : 3.803 18.027 1987 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.46 % Allowed : 12.93 % Favored : 86.61 % 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: 0.33 (0.20), residues: 1797 helix: 2.13 (0.23), residues: 502 sheet: -0.01 (0.23), residues: 485 loop : -0.85 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.004 0.001 HIS B 64 PHE 0.007 0.001 PHE A 663 TYR 0.010 0.001 TYR D 184 ARG 0.002 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 619) hydrogen bonds : angle 5.20795 ( 1752) SS BOND : bond 0.00044 ( 1) SS BOND : angle 1.06331 ( 2) covalent geometry : bond 0.00291 (14499) covalent geometry : angle 0.47181 (19680) Misc. bond : bond 0.00008 ( 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 113 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 2.329 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 outliers start: 7 outliers final: 6 residues processed: 112 average time/residue: 0.5438 time to fit residues: 93.3989 Evaluate side-chains 108 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 147 optimal weight: 0.0980 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 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: 0.9980 chunk 113 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.103148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071721 restraints weight = 130850.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074306 restraints weight = 48897.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075938 restraints weight = 27681.465| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14502 Z= 0.203 Angle : 0.495 6.564 19682 Z= 0.267 Chirality : 0.041 0.138 2155 Planarity : 0.003 0.044 2602 Dihedral : 3.846 17.664 1987 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.12 % Allowed : 12.93 % Favored : 85.95 % 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: 0.21 (0.20), residues: 1797 helix: 2.04 (0.23), residues: 507 sheet: -0.15 (0.23), residues: 486 loop : -0.91 (0.22), residues: 804 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 0.010 0.001 PHE A 72 TYR 0.010 0.001 TYR D 184 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 619) hydrogen bonds : angle 5.15919 ( 1752) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.30743 ( 2) covalent geometry : bond 0.00426 (14499) covalent geometry : angle 0.49493 (19680) Misc. bond : bond 0.00073 ( 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: 17 poor density : 100 time to evaluate : 2.347 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: 0.8138 (OUTLIER) cc_final: 0.7869 (mp10) outliers start: 17 outliers final: 10 residues processed: 116 average time/residue: 0.6342 time to fit residues: 115.0255 Evaluate side-chains 110 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 2.488 ------------------------------------------------------------------------------- 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 628 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.094840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.064388 restraints weight = 133321.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066896 restraints weight = 49807.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.068507 restraints weight = 28072.068| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1729 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= 0.153 Angle : 0.471 6.229 19682 Z= 0.253 Chirality : 0.041 0.135 2155 Planarity : 0.003 0.049 2602 Dihedral : 3.802 17.399 1987 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.92 % Allowed : 13.13 % Favored : 85.95 % 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: 0.28 (0.20), residues: 1797 helix: 2.18 (0.23), residues: 502 sheet: -0.21 (0.23), residues: 489 loop : -0.82 (0.22), residues: 806 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 0.008 0.000 ARG F 418 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 619) hydrogen bonds : angle 5.00335 ( 1752) SS BOND : bond 0.00231 ( 1) SS BOND : angle 1.17646 ( 2) covalent geometry : bond 0.00323 (14499) covalent geometry : angle 0.47075 (19680) Misc. bond : bond 0.00017 ( 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 116 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 2.436 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: 0.8094 (OUTLIER) cc_final: 0.7849 (mp10) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.5529 time to fit residues: 96.9867 Evaluate side-chains 114 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 2.371 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 84 optimal weight: 4.9990 chunk 120 optimal weight: 0.0060 chunk 133 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.095106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.064873 restraints weight = 132215.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067397 restraints weight = 48391.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.069006 restraints weight = 26938.786| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1798 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= 0.136 Angle : 0.464 6.532 19682 Z= 0.247 Chirality : 0.041 0.136 2155 Planarity : 0.003 0.044 2602 Dihedral : 3.750 17.118 1987 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.92 % Allowed : 13.33 % Favored : 85.75 % 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: 0.34 (0.20), residues: 1797 helix: 2.32 (0.23), residues: 493 sheet: -0.21 (0.23), residues: 489 loop : -0.79 (0.22), residues: 815 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 0.010 0.001 TYR D 184 ARG 0.002 0.000 ARG F 207 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 619) hydrogen bonds : angle 4.89336 ( 1752) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.22992 ( 2) covalent geometry : bond 0.00289 (14499) covalent geometry : angle 0.46349 (19680) Misc. bond : bond 0.00021 ( 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 121 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 2.345 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: 0.8103 (OUTLIER) cc_final: 0.7852 (mp10) outliers start: 14 outliers final: 12 residues processed: 119 average time/residue: 0.5394 time to fit residues: 99.1592 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 : 2.116 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 153 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.104046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072869 restraints weight = 130239.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075504 restraints weight = 48198.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077169 restraints weight = 27054.368| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14502 Z= 0.109 Angle : 0.456 6.121 19682 Z= 0.241 Chirality : 0.041 0.139 2155 Planarity : 0.003 0.046 2602 Dihedral : 3.701 16.828 1987 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.98 % Allowed : 13.39 % Favored : 85.62 % 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: 0.43 (0.20), residues: 1797 helix: 2.40 (0.23), residues: 493 sheet: -0.17 (0.23), residues: 482 loop : -0.73 (0.22), residues: 822 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 0.001 0.000 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 619) hydrogen bonds : angle 4.77825 ( 1752) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.16687 ( 2) covalent geometry : bond 0.00235 (14499) covalent geometry : angle 0.45549 (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 122 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 2.367 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: 0.8108 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: B 282 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8084 (mm-30) outliers start: 15 outliers final: 13 residues processed: 119 average time/residue: 0.5384 time to fit residues: 98.6470 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 : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE 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 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 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: 5.9990 chunk 174 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.102777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.071718 restraints weight = 131289.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074241 restraints weight = 50379.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075854 restraints weight = 28816.069| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14502 Z= 0.233 Angle : 0.509 6.336 19682 Z= 0.275 Chirality : 0.041 0.132 2155 Planarity : 0.003 0.042 2602 Dihedral : 3.837 15.983 1987 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.05 % Allowed : 13.39 % Favored : 85.55 % 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: 0.17 (0.20), residues: 1797 helix: 2.14 (0.23), residues: 496 sheet: -0.29 (0.23), residues: 486 loop : -0.89 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 745 HIS 0.003 0.001 HIS B 64 PHE 0.015 0.001 PHE A 652 TYR 0.010 0.001 TYR D 184 ARG 0.002 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 619) hydrogen bonds : angle 5.01099 ( 1752) SS BOND : bond 0.00349 ( 1) SS BOND : angle 1.32989 ( 2) covalent geometry : bond 0.00489 (14499) covalent geometry : angle 0.50861 (19680) Misc. bond : bond 0.00082 ( 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 122 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 2.666 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: A 403 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7984 (mp10) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.7007 time to fit residues: 133.5242 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 : 3.346 ------------------------------------------------------------------------------- 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 599 VAL Chi-restraints excluded: chain A residue 628 VAL 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 44 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.103539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072410 restraints weight = 130595.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.075025 restraints weight = 48583.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076684 restraints weight = 27360.943| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2052 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= 0.137 Angle : 0.473 6.314 19682 Z= 0.252 Chirality : 0.041 0.137 2155 Planarity : 0.003 0.049 2602 Dihedral : 3.779 16.100 1987 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.92 % Allowed : 13.79 % 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: 0.32 (0.20), residues: 1797 helix: 2.33 (0.23), residues: 493 sheet: -0.23 (0.23), residues: 481 loop : -0.81 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.002 0.001 HIS B 64 PHE 0.008 0.001 PHE A 652 TYR 0.011 0.001 TYR A 688 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 619) hydrogen bonds : angle 4.83818 ( 1752) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.21227 ( 2) covalent geometry : bond 0.00292 (14499) covalent geometry : angle 0.47333 (19680) Misc. bond : bond 0.00014 ( 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 116 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 2.835 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: 0.8166 (OUTLIER) cc_final: 0.7918 (mp10) outliers start: 14 outliers final: 12 residues processed: 114 average time/residue: 0.7545 time to fit residues: 136.7892 Evaluate side-chains 115 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 2.854 ------------------------------------------------------------------------------- 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 563 ASN 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 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: 7.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.094593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064190 restraints weight = 132429.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066710 restraints weight = 48893.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068312 restraints weight = 27431.015| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2122 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= 0.148 Angle : 0.472 6.155 19682 Z= 0.252 Chirality : 0.041 0.135 2155 Planarity : 0.003 0.041 2602 Dihedral : 3.755 15.701 1987 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.92 % Allowed : 13.72 % Favored : 85.36 % 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: 0.33 (0.20), residues: 1797 helix: 2.35 (0.23), residues: 493 sheet: -0.23 (0.23), residues: 481 loop : -0.81 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.003 0.001 HIS B 64 PHE 0.007 0.001 PHE A 652 TYR 0.010 0.001 TYR D 184 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 619) hydrogen bonds : angle 4.83578 ( 1752) SS BOND : bond 0.00309 ( 1) SS BOND : angle 1.26497 ( 2) covalent geometry : bond 0.00315 (14499) covalent geometry : angle 0.47230 (19680) Misc. bond : bond 0.00028 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8319.01 seconds wall clock time: 147 minutes 58.91 seconds (8878.91 seconds total)