Starting phenix.real_space_refine on Tue Mar 3 17:46:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3r_13185/03_2026/7p3r_13185.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3r_13185/03_2026/7p3r_13185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2026/7p3r_13185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2026/7p3r_13185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2026/7p3r_13185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2026/7p3r_13185.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 4702 2.51 5 N 1454 2.21 5 O 1574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7738 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1902 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 6, 'TRANS': 321} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 722 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'PHE:plan': 7, 'GLN:plan1': 11, 'HIS:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 19, 'TRP:plan': 5, 'GLU:plan': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 273 Chain: "B" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 1967 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 6, 'TRANS': 334} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 590 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 15, 'PHE:plan': 7, 'HIS:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 19, 'TRP:plan': 5, 'GLU:plan': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 289 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1902 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 6, 'TRANS': 321} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 722 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'PHE:plan': 7, 'GLN:plan1': 11, 'HIS:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 19, 'TRP:plan': 5, 'GLU:plan': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 273 Chain: "D" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 1967 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 6, 'TRANS': 334} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 590 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 15, 'PHE:plan': 7, 'HIS:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 19, 'TRP:plan': 5, 'GLU:plan': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 289 Time building chain proxies: 2.11, per 1000 atoms: 0.27 Number of scatterers: 7738 At special positions: 0 Unit cell: (157.342, 128.166, 110.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1574 8.00 N 1454 7.00 C 4702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 380.9 milliseconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.964A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.185A pdb=" N LYS A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.532A pdb=" N ILE A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 101 removed outlier: 3.675A pdb=" N ALA A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 158 removed outlier: 4.124A pdb=" N ILE A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 217 removed outlier: 3.904A pdb=" N TYR A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 315 removed outlier: 3.863A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 345 removed outlier: 4.382A pdb=" N ILE A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 35 removed outlier: 3.694A pdb=" N THR B 15 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.663A pdb=" N ALA B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.656A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 98 removed outlier: 4.025A pdb=" N VAL B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 157 removed outlier: 3.514A pdb=" N GLN B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 217 removed outlier: 4.073A pdb=" N TYR B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 319 removed outlier: 3.560A pdb=" N ALA B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 328 removed outlier: 3.631A pdb=" N ILE B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 349 removed outlier: 4.193A pdb=" N LYS B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 35 Processing helix chain 'C' and resid 46 through 67 Processing helix chain 'C' and resid 67 through 85 removed outlier: 3.965A pdb=" N ILE C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Proline residue: C 77 - end of helix removed outlier: 3.812A pdb=" N ASN C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 101 removed outlier: 3.577A pdb=" N TYR C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 126 removed outlier: 3.784A pdb=" N SER C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 216 removed outlier: 3.981A pdb=" N ASN C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 316 removed outlier: 4.102A pdb=" N ILE C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 272 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 301 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 345 removed outlier: 6.171A pdb=" N LYS C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL C 330 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 343 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 35 removed outlier: 3.580A pdb=" N VAL D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 67 removed outlier: 4.152A pdb=" N LYS D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D 67 " --> pdb=" O GLN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.890A pdb=" N SER D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.584A pdb=" N ALA D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 156 removed outlier: 3.992A pdb=" N ASP D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 218 removed outlier: 3.910A pdb=" N PHE D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 319 removed outlier: 3.629A pdb=" N ALA D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 328 removed outlier: 3.936A pdb=" N ILE D 326 " --> pdb=" O MET D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 349 removed outlier: 4.015A pdb=" N VAL D 343 " --> pdb=" O TRP D 339 " (cutoff:3.500A) 937 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2589 1.34 - 1.45: 578 1.45 - 1.57: 4571 1.57 - 1.68: 0 1.68 - 1.80: 16 Bond restraints: 7754 Sorted by residual: bond pdb=" C ILE C 76 " pdb=" N PRO C 77 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.25e-02 6.40e+03 1.60e+01 bond pdb=" CB THR C 242 " pdb=" CG2 THR C 242 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.69e+00 bond pdb=" CB ILE A 237 " pdb=" CG2 ILE A 237 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.30e+00 bond pdb=" CB ILE A 236 " pdb=" CG2 ILE A 236 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CB VAL D 208 " pdb=" CG1 VAL D 208 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10364 1.99 - 3.97: 297 3.97 - 5.96: 23 5.96 - 7.94: 3 7.94 - 9.93: 3 Bond angle restraints: 10690 Sorted by residual: angle pdb=" C PHE B 37 " pdb=" N THR B 38 " pdb=" CA THR B 38 " ideal model delta sigma weight residual 120.69 130.62 -9.93 2.95e+00 1.15e-01 1.13e+01 angle pdb=" N ILE A 76 " pdb=" CA ILE A 76 " pdb=" C ILE A 76 " ideal model delta sigma weight residual 108.88 115.88 -7.00 2.16e+00 2.14e-01 1.05e+01 angle pdb=" C ASP A 252 " pdb=" N ASP A 253 " pdb=" CA ASP A 253 " ideal model delta sigma weight residual 122.06 116.16 5.90 1.86e+00 2.89e-01 1.01e+01 angle pdb=" N ILE C 76 " pdb=" CA ILE C 76 " pdb=" C ILE C 76 " ideal model delta sigma weight residual 108.88 115.72 -6.84 2.16e+00 2.14e-01 1.00e+01 angle pdb=" N VAL D 155 " pdb=" CA VAL D 155 " pdb=" CB VAL D 155 " ideal model delta sigma weight residual 111.75 103.19 8.56 2.73e+00 1.34e-01 9.84e+00 ... (remaining 10685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4337 17.38 - 34.76: 214 34.76 - 52.14: 44 52.14 - 69.52: 8 69.52 - 86.90: 11 Dihedral angle restraints: 4614 sinusoidal: 748 harmonic: 3866 Sorted by residual: dihedral pdb=" CA ASP D 84 " pdb=" C ASP D 84 " pdb=" N ALA D 85 " pdb=" CA ALA D 85 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA LEU D 50 " pdb=" C LEU D 50 " pdb=" N SER D 51 " pdb=" CA SER D 51 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ASP D 67 " pdb=" C ASP D 67 " pdb=" N LEU D 68 " pdb=" CA LEU D 68 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1124 0.056 - 0.112: 247 0.112 - 0.168: 38 0.168 - 0.224: 7 0.224 - 0.280: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CB ILE A 236 " pdb=" CA ILE A 236 " pdb=" CG1 ILE A 236 " pdb=" CG2 ILE A 236 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VAL D 208 " pdb=" CA VAL D 208 " pdb=" CG1 VAL D 208 " pdb=" CG2 VAL D 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE C 236 " pdb=" CA ILE C 236 " pdb=" CG1 ILE C 236 " pdb=" CG2 ILE C 236 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1415 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 237 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C ILE A 237 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A 237 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 238 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 62 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C LYS B 62 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS B 62 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN B 63 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 208 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C VAL D 208 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL D 208 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA D 209 " -0.013 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2591 2.83 - 3.34: 7795 3.34 - 3.86: 12977 3.86 - 4.38: 13335 4.38 - 4.90: 22463 Nonbonded interactions: 59161 Sorted by model distance: nonbonded pdb=" O ALA D 221 " pdb=" OG SER D 225 " model vdw 2.306 3.040 nonbonded pdb=" O ALA B 238 " pdb=" OG1 THR B 242 " model vdw 2.312 3.040 nonbonded pdb=" O GLY A 210 " pdb=" OG1 THR A 214 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR B 214 " pdb=" OG SER B 225 " model vdw 2.348 3.040 nonbonded pdb=" O TRP A 64 " pdb=" N GLY A 69 " model vdw 2.351 3.120 ... (remaining 59156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 19 through 346) selection = chain 'C' selection = (chain 'D' and resid 19 through 346) } 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: 6.610 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.800 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 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 : 0.006 0.085 7754 Z= 0.281 Angle : 0.806 9.928 10690 Z= 0.508 Chirality : 0.049 0.280 1418 Planarity : 0.006 0.023 1486 Dihedral : 13.657 86.902 2090 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.28 % Allowed : 9.55 % Favored : 90.17 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.17), residues: 1330 helix: -2.13 (0.11), residues: 1151 sheet: None (None), residues: 0 loop : -2.75 (0.38), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 183 TYR 0.010 0.002 TYR C 254 PHE 0.007 0.001 PHE A 205 TRP 0.009 0.001 TRP B 243 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 7754) covalent geometry : angle 0.80581 (10690) hydrogen bonds : bond 0.11882 ( 937) hydrogen bonds : angle 6.20436 ( 2811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.301 Fit side-chains REVERT: A 163 LYS cc_start: 0.8007 (mttt) cc_final: 0.7743 (mtpt) REVERT: A 187 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 248 ASN cc_start: 0.8239 (t0) cc_final: 0.7511 (m-40) REVERT: B 171 ASP cc_start: 0.8350 (t70) cc_final: 0.8031 (t70) REVERT: B 173 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 272 ILE cc_start: 0.8700 (pt) cc_final: 0.8498 (mm) REVERT: C 160 ASN cc_start: 0.7470 (m-40) cc_final: 0.7261 (m-40) REVERT: C 191 LYS cc_start: 0.8923 (tptt) cc_final: 0.8628 (tppt) REVERT: D 251 ASP cc_start: 0.7231 (m-30) cc_final: 0.6820 (m-30) REVERT: D 275 GLN cc_start: 0.6985 (tp40) cc_final: 0.6608 (mm110) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.0732 time to fit residues: 11.9799 Evaluate side-chains 95 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN C 177 ASN C 248 ASN C 249 GLN C 270 GLN D 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.189008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.184501 restraints weight = 11656.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.184442 restraints weight = 18865.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.184351 restraints weight = 18374.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.184265 restraints weight = 17452.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.184202 restraints weight = 16825.029| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7754 Z= 0.152 Angle : 0.444 4.858 10690 Z= 0.272 Chirality : 0.036 0.146 1418 Planarity : 0.003 0.016 1486 Dihedral : 4.703 20.659 1346 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.25 % Allowed : 17.70 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1330 helix: 0.16 (0.14), residues: 1151 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 183 TYR 0.008 0.001 TYR B 254 PHE 0.010 0.001 PHE A 205 TRP 0.003 0.000 TRP B 243 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7754) covalent geometry : angle 0.44380 (10690) hydrogen bonds : bond 0.04351 ( 937) hydrogen bonds : angle 3.96927 ( 2811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8072 (t0) cc_final: 0.7732 (m-40) REVERT: B 272 ILE cc_start: 0.8306 (pt) cc_final: 0.8095 (mm) REVERT: C 213 LEU cc_start: 0.9036 (tp) cc_final: 0.8807 (tp) REVERT: C 228 ILE cc_start: 0.9378 (mm) cc_final: 0.9148 (mt) REVERT: D 175 MET cc_start: 0.6892 (mmt) cc_final: 0.6678 (mmt) REVERT: D 191 LYS cc_start: 0.8286 (mptt) cc_final: 0.8066 (mppt) REVERT: D 251 ASP cc_start: 0.6769 (m-30) cc_final: 0.6541 (m-30) outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.0748 time to fit residues: 12.3613 Evaluate side-chains 108 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 50.0000 chunk 100 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN C 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.178112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.164363 restraints weight = 11570.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.164143 restraints weight = 22267.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.163715 restraints weight = 21827.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.162991 restraints weight = 18413.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.162707 restraints weight = 16712.269| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7754 Z= 0.233 Angle : 0.508 5.703 10690 Z= 0.303 Chirality : 0.040 0.176 1418 Planarity : 0.003 0.016 1486 Dihedral : 4.619 23.921 1346 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.49 % Allowed : 19.66 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1330 helix: 0.95 (0.14), residues: 1152 sheet: None (None), residues: 0 loop : -1.64 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 183 TYR 0.009 0.002 TYR D 254 PHE 0.012 0.001 PHE A 205 TRP 0.008 0.001 TRP A 243 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 7754) covalent geometry : angle 0.50841 (10690) hydrogen bonds : bond 0.04469 ( 937) hydrogen bonds : angle 3.87888 ( 2811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 237 ILE cc_start: 0.8501 (tp) cc_final: 0.8285 (mt) REVERT: B 272 ILE cc_start: 0.8588 (pt) cc_final: 0.8313 (mm) REVERT: D 191 LYS cc_start: 0.8395 (mptt) cc_final: 0.8178 (mppt) REVERT: D 251 ASP cc_start: 0.6881 (m-30) cc_final: 0.6528 (m-30) outliers start: 16 outliers final: 9 residues processed: 107 average time/residue: 0.0712 time to fit residues: 10.9797 Evaluate side-chains 105 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 50.0000 chunk 113 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 50.0000 chunk 43 optimal weight: 60.0000 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 50.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.184018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.179637 restraints weight = 11748.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.179556 restraints weight = 23063.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.179230 restraints weight = 22597.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.178809 restraints weight = 25980.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.178642 restraints weight = 20953.778| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7754 Z= 0.201 Angle : 0.463 5.530 10690 Z= 0.277 Chirality : 0.038 0.172 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.396 20.918 1346 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.34 % Allowed : 23.31 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.22), residues: 1330 helix: 1.47 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 183 TYR 0.011 0.001 TYR D 254 PHE 0.010 0.001 PHE A 205 TRP 0.008 0.001 TRP B 243 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 7754) covalent geometry : angle 0.46311 (10690) hydrogen bonds : bond 0.04282 ( 937) hydrogen bonds : angle 3.69573 ( 2811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 237 ILE cc_start: 0.8699 (tp) cc_final: 0.8495 (mt) REVERT: A 259 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B 272 ILE cc_start: 0.8446 (pt) cc_final: 0.8180 (mm) REVERT: C 206 MET cc_start: 0.8579 (mtm) cc_final: 0.8284 (mtt) outliers start: 19 outliers final: 12 residues processed: 109 average time/residue: 0.0741 time to fit residues: 11.7177 Evaluate side-chains 101 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 0.9990 chunk 104 optimal weight: 50.0000 chunk 105 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 95 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 40.0000 chunk 91 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.178519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.164617 restraints weight = 11671.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.164458 restraints weight = 20769.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.163978 restraints weight = 18855.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.162673 restraints weight = 21006.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.162199 restraints weight = 18769.054| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7754 Z= 0.162 Angle : 0.426 4.718 10690 Z= 0.255 Chirality : 0.037 0.172 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.110 20.779 1346 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.06 % Allowed : 25.00 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.22), residues: 1330 helix: 1.99 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.36 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 183 TYR 0.010 0.001 TYR D 254 PHE 0.008 0.001 PHE A 205 TRP 0.006 0.001 TRP B 243 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7754) covalent geometry : angle 0.42572 (10690) hydrogen bonds : bond 0.04039 ( 937) hydrogen bonds : angle 3.48367 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8254 (t0) cc_final: 0.7702 (m-40) REVERT: B 272 ILE cc_start: 0.8672 (pt) cc_final: 0.8287 (mm) outliers start: 18 outliers final: 15 residues processed: 115 average time/residue: 0.0726 time to fit residues: 12.1231 Evaluate side-chains 104 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 79 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 40.0000 chunk 46 optimal weight: 50.0000 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 50.0000 chunk 86 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.181110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.176817 restraints weight = 11823.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.176518 restraints weight = 23314.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.176222 restraints weight = 24209.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.175862 restraints weight = 22846.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175706 restraints weight = 21636.645| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 7754 Z= 0.255 Angle : 0.534 8.325 10690 Z= 0.314 Chirality : 0.040 0.182 1418 Planarity : 0.002 0.016 1486 Dihedral : 4.549 24.340 1346 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 7.02 % Allowed : 24.44 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.22), residues: 1330 helix: 1.65 (0.14), residues: 1166 sheet: None (None), residues: 0 loop : -1.38 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 183 TYR 0.011 0.002 TYR D 254 PHE 0.012 0.001 PHE A 205 TRP 0.010 0.001 TRP D 243 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 7754) covalent geometry : angle 0.53424 (10690) hydrogen bonds : bond 0.04542 ( 937) hydrogen bonds : angle 3.88479 ( 2811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: D 251 ASP cc_start: 0.6843 (m-30) cc_final: 0.6537 (m-30) outliers start: 25 outliers final: 17 residues processed: 111 average time/residue: 0.0669 time to fit residues: 11.0085 Evaluate side-chains 104 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 60 optimal weight: 50.0000 chunk 33 optimal weight: 30.0000 chunk 79 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.179903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.175518 restraints weight = 11894.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.175398 restraints weight = 26096.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.175130 restraints weight = 23035.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.174861 restraints weight = 24187.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.174725 restraints weight = 20308.136| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 7754 Z= 0.287 Angle : 0.568 8.643 10690 Z= 0.332 Chirality : 0.042 0.189 1418 Planarity : 0.003 0.017 1486 Dihedral : 4.740 24.963 1346 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.74 % Allowed : 26.69 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.22), residues: 1330 helix: 1.44 (0.14), residues: 1162 sheet: None (None), residues: 0 loop : -1.47 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 183 TYR 0.010 0.002 TYR D 254 PHE 0.009 0.001 PHE A 205 TRP 0.011 0.002 TRP B 243 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 7754) covalent geometry : angle 0.56842 (10690) hydrogen bonds : bond 0.04677 ( 937) hydrogen bonds : angle 4.05982 ( 2811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.267 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 106 average time/residue: 0.0698 time to fit residues: 10.8131 Evaluate side-chains 108 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 50.0000 chunk 93 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 43 optimal weight: 60.0000 chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 overall best weight: 7.5592 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.178686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.174287 restraints weight = 11932.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.173904 restraints weight = 23695.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.173693 restraints weight = 26570.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.173344 restraints weight = 20228.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.173182 restraints weight = 25176.976| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 7754 Z= 0.307 Angle : 0.589 10.053 10690 Z= 0.345 Chirality : 0.042 0.189 1418 Planarity : 0.003 0.024 1486 Dihedral : 4.950 25.517 1346 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 8.15 % Allowed : 26.40 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1330 helix: 1.29 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.86 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 183 TYR 0.009 0.002 TYR D 254 PHE 0.013 0.001 PHE A 205 TRP 0.015 0.002 TRP D 243 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 7754) covalent geometry : angle 0.58947 (10690) hydrogen bonds : bond 0.04859 ( 937) hydrogen bonds : angle 4.22132 ( 2811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: D 251 ASP cc_start: 0.6842 (m-30) cc_final: 0.6574 (m-30) outliers start: 29 outliers final: 23 residues processed: 114 average time/residue: 0.0685 time to fit residues: 11.6086 Evaluate side-chains 117 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 96 optimal weight: 50.0000 chunk 76 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.183544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.179193 restraints weight = 11731.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.178967 restraints weight = 19238.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.178850 restraints weight = 20229.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.178703 restraints weight = 18420.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.178620 restraints weight = 20232.666| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7754 Z= 0.132 Angle : 0.441 5.400 10690 Z= 0.260 Chirality : 0.036 0.192 1418 Planarity : 0.002 0.015 1486 Dihedral : 4.206 18.820 1346 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.06 % Allowed : 29.78 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.23), residues: 1330 helix: 2.19 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -1.51 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 183 TYR 0.007 0.001 TYR D 254 PHE 0.007 0.001 PHE A 205 TRP 0.008 0.001 TRP D 243 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7754) covalent geometry : angle 0.44119 (10690) hydrogen bonds : bond 0.04061 ( 937) hydrogen bonds : angle 3.60729 ( 2811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8231 (t0) cc_final: 0.7698 (m-40) REVERT: B 191 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7992 (mmtp) outliers start: 18 outliers final: 16 residues processed: 107 average time/residue: 0.0715 time to fit residues: 11.3375 Evaluate side-chains 111 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 50.0000 chunk 77 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 96 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 128 optimal weight: 50.0000 chunk 67 optimal weight: 40.0000 chunk 61 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.182582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.178266 restraints weight = 11671.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.178060 restraints weight = 20713.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.177935 restraints weight = 21377.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.177776 restraints weight = 18444.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.177651 restraints weight = 21354.948| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7754 Z= 0.153 Angle : 0.453 6.427 10690 Z= 0.264 Chirality : 0.037 0.168 1418 Planarity : 0.002 0.017 1486 Dihedral : 4.102 21.183 1346 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.34 % Allowed : 28.65 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.23), residues: 1330 helix: 2.38 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -1.47 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 183 TYR 0.009 0.001 TYR D 254 PHE 0.009 0.001 PHE A 205 TRP 0.007 0.001 TRP D 243 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7754) covalent geometry : angle 0.45281 (10690) hydrogen bonds : bond 0.04050 ( 937) hydrogen bonds : angle 3.52664 ( 2811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.267 Fit side-chains REVERT: A 248 ASN cc_start: 0.8258 (t0) cc_final: 0.7720 (m-40) REVERT: B 191 LYS cc_start: 0.8232 (mmtt) cc_final: 0.8003 (mmtp) outliers start: 19 outliers final: 16 residues processed: 108 average time/residue: 0.0696 time to fit residues: 11.0108 Evaluate side-chains 115 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 50.0000 chunk 111 optimal weight: 50.0000 chunk 119 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.181022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.177074 restraints weight = 12009.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.176788 restraints weight = 20352.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.176335 restraints weight = 21285.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.176169 restraints weight = 21262.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.175971 restraints weight = 17376.348| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7754 Z= 0.118 Angle : 0.423 6.061 10690 Z= 0.247 Chirality : 0.036 0.183 1418 Planarity : 0.002 0.015 1486 Dihedral : 3.823 17.096 1346 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.81 % Allowed : 31.18 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.23), residues: 1330 helix: 2.78 (0.14), residues: 1167 sheet: None (None), residues: 0 loop : -1.34 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 183 TYR 0.008 0.001 TYR D 254 PHE 0.006 0.000 PHE A 205 TRP 0.006 0.001 TRP D 243 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 7754) covalent geometry : angle 0.42275 (10690) hydrogen bonds : bond 0.03780 ( 937) hydrogen bonds : angle 3.29910 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1378.04 seconds wall clock time: 24 minutes 19.39 seconds (1459.39 seconds total)