Starting phenix.real_space_refine on Sat Aug 23 16:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0d_36761/08_2025/8k0d_36761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0d_36761/08_2025/8k0d_36761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k0d_36761/08_2025/8k0d_36761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0d_36761/08_2025/8k0d_36761.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k0d_36761/08_2025/8k0d_36761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0d_36761/08_2025/8k0d_36761.map" } resolution = 2.94 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= 0.009 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 64 5.16 5 C 8414 2.51 5 N 2222 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13282 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Chain: "C" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Time building chain proxies: 3.81, per 1000 atoms: 0.29 Number of scatterers: 13282 At special positions: 0 Unit cell: (125.46, 99.22, 214.84, 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 64 16.00 O 2582 8.00 N 2222 7.00 C 8414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " 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=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 690.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 37 sheets defined 6.2% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.662A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'F' and resid 120 through 127 removed outlier: 3.547A pdb=" N GLY F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.644A pdb=" N LEU A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.709A pdb=" N GLN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.577A pdb=" N THR C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.146A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'B' and resid 204 through 207 removed outlier: 3.561A pdb=" N LEU B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 204 through 207' Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.553A pdb=" N GLN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.569A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.647A pdb=" N ARG E 34 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.968A pdb=" N VAL E 118 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR E 101 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE E 116 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR E 103 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN E 114 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.585A pdb=" N VAL E 200 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AA6, first strand: chain 'E' and resid 185 through 186 removed outlier: 3.535A pdb=" N VAL E 185 " --> pdb=" O SER E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.811A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.082A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.517A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 132 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 152 through 153 removed outlier: 3.705A pdb=" N LYS F 144 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 196 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN F 146 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F 206 " --> pdb=" O CYS F 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 202 removed outlier: 5.435A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AB4, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.045A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 287 removed outlier: 5.460A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A 313 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET A 316 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 318 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 333 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.308A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.308A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.581A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.423A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.630A pdb=" N VAL C 123 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG C 34 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TRP C 35 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 51 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP C 37 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.630A pdb=" N VAL C 123 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS C 97 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 119 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG C 99 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.504A pdb=" N GLY C 155 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.504A pdb=" N GLY C 155 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 197 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS C 180 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.615A pdb=" N LYS C 225 " --> pdb=" O CYS C 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.058A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.536A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 113 through 117 removed outlier: 3.664A pdb=" N SER D 176 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR D 172 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.418A pdb=" N TRP D 147 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 208 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS D 206 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 201 through 202 removed outlier: 5.382A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AD5, first strand: chain 'B' and resid 217 through 218 removed outlier: 6.488A pdb=" N TYR B 231 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 250 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS B 233 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG B 248 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 235 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 244 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 279 through 287 removed outlier: 5.589A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 313 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.357A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.357A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.522A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 511 through 515 removed outlier: 6.397A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1254 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: 2.06 Time building geometry restraints manager: 1.42 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: 4237 1.34 - 1.46: 3144 1.46 - 1.58: 6161 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 13624 Sorted by residual: bond pdb=" C LYS A 443 " pdb=" N ILE A 444 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.48e-02 4.57e+03 2.14e+00 bond pdb=" C LYS B 443 " pdb=" N ILE B 444 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.48e-02 4.57e+03 2.08e+00 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.37e+00 bond pdb=" CA SER C 106 " pdb=" C SER C 106 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.19e+00 bond pdb=" CA SER E 106 " pdb=" C SER E 106 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.17e+00 ... (remaining 13619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 18257 2.13 - 4.27: 282 4.27 - 6.40: 20 6.40 - 8.54: 0 8.54 - 10.67: 1 Bond angle restraints: 18560 Sorted by residual: angle pdb=" N ARG A 402 " pdb=" CA ARG A 402 " pdb=" C ARG A 402 " ideal model delta sigma weight residual 110.40 99.73 10.67 1.43e+00 4.89e-01 5.57e+01 angle pdb=" N VAL A 484 " pdb=" CA VAL A 484 " pdb=" C VAL A 484 " ideal model delta sigma weight residual 113.71 110.17 3.54 9.50e-01 1.11e+00 1.38e+01 angle pdb=" C TYR F 185 " pdb=" N GLU F 186 " pdb=" CA GLU F 186 " ideal model delta sigma weight residual 122.38 116.69 5.69 1.81e+00 3.05e-01 9.87e+00 angle pdb=" N ILE A 401 " pdb=" CA ILE A 401 " pdb=" C ILE A 401 " ideal model delta sigma weight residual 110.42 113.24 -2.82 9.60e-01 1.09e+00 8.66e+00 angle pdb=" C PHE A 290 " pdb=" N TYR A 291 " pdb=" CA TYR A 291 " ideal model delta sigma weight residual 122.86 118.76 4.10 1.42e+00 4.96e-01 8.35e+00 ... (remaining 18555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7716 17.93 - 35.86: 364 35.86 - 53.79: 61 53.79 - 71.71: 12 71.71 - 89.64: 9 Dihedral angle restraints: 8162 sinusoidal: 3184 harmonic: 4978 Sorted by residual: dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual -86.00 -175.64 89.64 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS A 216 " pdb=" SG CYS A 216 " pdb=" SG CYS A 240 " pdb=" CB CYS A 240 " ideal model delta sinusoidal sigma weight residual 93.00 178.38 -85.38 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS B 216 " pdb=" SG CYS B 216 " pdb=" SG CYS B 240 " pdb=" CB CYS B 240 " ideal model delta sinusoidal sigma weight residual 93.00 174.35 -81.35 1 1.00e+01 1.00e-02 8.16e+01 ... (remaining 8159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1543 0.046 - 0.093: 370 0.093 - 0.139: 149 0.139 - 0.186: 0 0.186 - 0.232: 2 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CB ILE B 408 " pdb=" CA ILE B 408 " pdb=" CG1 ILE B 408 " pdb=" CG2 ILE B 408 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 408 " pdb=" CA ILE A 408 " pdb=" CG1 ILE A 408 " pdb=" CG2 ILE A 408 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE B 250 " pdb=" N ILE B 250 " pdb=" C ILE B 250 " pdb=" CB ILE B 250 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2061 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 291 " -0.018 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR B 291 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 291 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 291 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 291 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 291 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 291 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 291 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 164 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO E 165 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 165 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 165 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.018 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR A 351 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.001 2.00e-02 2.50e+03 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 200 2.63 - 3.20: 11875 3.20 - 3.77: 21302 3.77 - 4.33: 30453 4.33 - 4.90: 50325 Nonbonded interactions: 114155 Sorted by model distance: nonbonded pdb=" OG SER B 528 " pdb=" O THR B 531 " model vdw 2.065 3.040 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE2 GLU F 81 " model vdw 2.153 3.120 nonbonded pdb=" O LEU A 202 " pdb=" NH2 ARG B 258 " model vdw 2.177 3.120 nonbonded pdb=" OE1 GLU D 105 " pdb=" OH TYR D 172 " model vdw 2.203 3.040 nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 22 " model vdw 2.212 3.040 ... (remaining 114150 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.890 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 14.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.004 0.034 13646 Z= 0.181 Angle : 0.628 10.669 18604 Z= 0.354 Chirality : 0.046 0.232 2064 Planarity : 0.004 0.054 2380 Dihedral : 10.650 84.238 4916 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.58 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.20), residues: 1702 helix: -2.82 (0.62), residues: 44 sheet: -1.34 (0.19), residues: 696 loop : -0.63 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 402 TYR 0.039 0.002 TYR B 291 PHE 0.020 0.002 PHE F 83 TRP 0.014 0.001 TRP C 170 HIS 0.004 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00389 (13624) covalent geometry : angle 0.62796 (18560) SS BOND : bond 0.00176 ( 22) SS BOND : angle 0.78158 ( 44) hydrogen bonds : bond 0.26170 ( 426) hydrogen bonds : angle 11.34261 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: E 30 SER cc_start: 0.7993 (t) cc_final: 0.7790 (t) REVERT: E 213 ASN cc_start: 0.7647 (m110) cc_final: 0.7307 (m-40) REVERT: E 215 ASN cc_start: 0.8023 (t0) cc_final: 0.7640 (t0) REVERT: E 222 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7524 (mmmm) REVERT: F 116 ILE cc_start: 0.8400 (tt) cc_final: 0.7549 (mp) REVERT: F 159 GLN cc_start: 0.8471 (mp10) cc_final: 0.8097 (mp10) REVERT: F 169 ASP cc_start: 0.8672 (p0) cc_final: 0.7843 (p0) REVERT: A 463 MET cc_start: 0.8083 (mmt) cc_final: 0.7858 (mmm) REVERT: C 160 ASP cc_start: 0.8656 (m-30) cc_final: 0.8425 (p0) REVERT: D 82 ASP cc_start: 0.7926 (m-30) cc_final: 0.7624 (m-30) REVERT: D 160 GLU cc_start: 0.8047 (tp30) cc_final: 0.7808 (tp30) REVERT: B 399 MET cc_start: 0.8870 (tpp) cc_final: 0.8583 (tpp) REVERT: B 555 ASP cc_start: 0.8418 (p0) cc_final: 0.7839 (t0) outliers start: 0 outliers final: 1 residues processed: 165 average time/residue: 0.6200 time to fit residues: 110.4958 Evaluate side-chains 104 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN E 213 ASN F 6 GLN A 564 ASN D 6 GLN B 269 ASN B 281 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.119628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.084102 restraints weight = 27676.984| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.71 r_work: 0.3425 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13646 Z= 0.168 Angle : 0.621 7.652 18604 Z= 0.328 Chirality : 0.047 0.164 2064 Planarity : 0.005 0.053 2380 Dihedral : 6.162 150.241 1857 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.93 % Allowed : 7.14 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.20), residues: 1702 helix: -2.67 (0.57), residues: 44 sheet: -1.20 (0.18), residues: 762 loop : -0.60 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 99 TYR 0.025 0.002 TYR A 351 PHE 0.023 0.002 PHE F 83 TRP 0.012 0.001 TRP E 48 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00376 (13624) covalent geometry : angle 0.62106 (18560) SS BOND : bond 0.00312 ( 22) SS BOND : angle 0.76990 ( 44) hydrogen bonds : bond 0.04490 ( 426) hydrogen bonds : angle 7.62188 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: E 222 LYS cc_start: 0.8521 (mmtt) cc_final: 0.7978 (mmmm) REVERT: F 17 ASP cc_start: 0.8556 (m-30) cc_final: 0.8200 (m-30) REVERT: F 169 ASP cc_start: 0.8798 (p0) cc_final: 0.8180 (p0) REVERT: C 99 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8255 (ttp80) REVERT: C 160 ASP cc_start: 0.8734 (m-30) cc_final: 0.8402 (p0) REVERT: D 82 ASP cc_start: 0.8207 (m-30) cc_final: 0.7943 (m-30) outliers start: 14 outliers final: 2 residues processed: 132 average time/residue: 0.5783 time to fit residues: 83.1425 Evaluate side-chains 93 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 166 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 137 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN F 136 ASN F 137 ASN A 269 ASN B 269 ASN B 586 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.119388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.085838 restraints weight = 27596.517| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.81 r_work: 0.3428 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13646 Z= 0.151 Angle : 0.583 7.492 18604 Z= 0.306 Chirality : 0.046 0.151 2064 Planarity : 0.005 0.051 2380 Dihedral : 4.949 54.240 1854 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.32 % Allowed : 9.33 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.20), residues: 1702 helix: -2.43 (0.61), residues: 44 sheet: -1.04 (0.18), residues: 794 loop : -0.53 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 18 TYR 0.019 0.001 TYR A 351 PHE 0.024 0.002 PHE D 117 TRP 0.020 0.001 TRP C 170 HIS 0.004 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00339 (13624) covalent geometry : angle 0.58194 (18560) SS BOND : bond 0.00426 ( 22) SS BOND : angle 0.91530 ( 44) hydrogen bonds : bond 0.03796 ( 426) hydrogen bonds : angle 6.84483 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.341 Fit side-chains REVERT: E 74 ASP cc_start: 0.8128 (t70) cc_final: 0.7760 (t70) REVERT: F 17 ASP cc_start: 0.8583 (m-30) cc_final: 0.8152 (m-30) REVERT: F 116 ILE cc_start: 0.8114 (tt) cc_final: 0.7212 (pp) REVERT: F 169 ASP cc_start: 0.8846 (p0) cc_final: 0.8309 (p0) REVERT: A 393 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7969 (pp20) REVERT: A 550 GLN cc_start: 0.7989 (tt0) cc_final: 0.7777 (tt0) REVERT: C 160 ASP cc_start: 0.8699 (m-30) cc_final: 0.8359 (p0) REVERT: D 17 ASP cc_start: 0.8053 (t0) cc_final: 0.7831 (t0) outliers start: 20 outliers final: 4 residues processed: 117 average time/residue: 0.5134 time to fit residues: 66.2842 Evaluate side-chains 92 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 349 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 ASN F 137 ASN A 269 ASN A 557 ASN C 5 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN B 332 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.112877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.077752 restraints weight = 27904.422| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.57 r_work: 0.3282 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 13646 Z= 0.397 Angle : 0.753 10.037 18604 Z= 0.392 Chirality : 0.051 0.189 2064 Planarity : 0.006 0.051 2380 Dihedral : 5.490 54.804 1854 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.45 % Allowed : 9.85 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.20), residues: 1702 helix: -1.88 (0.69), residues: 44 sheet: -0.98 (0.18), residues: 766 loop : -0.64 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 18 TYR 0.034 0.003 TYR B 292 PHE 0.025 0.003 PHE A 369 TRP 0.018 0.002 TRP C 170 HIS 0.005 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00919 (13624) covalent geometry : angle 0.75201 (18560) SS BOND : bond 0.00410 ( 22) SS BOND : angle 1.04047 ( 44) hydrogen bonds : bond 0.04286 ( 426) hydrogen bonds : angle 6.94181 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.520 Fit side-chains REVERT: E 74 ASP cc_start: 0.8465 (t70) cc_final: 0.7917 (t0) REVERT: F 24 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7681 (ttm110) REVERT: F 116 ILE cc_start: 0.8236 (tt) cc_final: 0.7327 (pp) REVERT: F 169 ASP cc_start: 0.8806 (p0) cc_final: 0.8426 (p0) REVERT: A 393 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8084 (pp20) REVERT: A 550 GLN cc_start: 0.8203 (tt0) cc_final: 0.7972 (tt0) REVERT: C 160 ASP cc_start: 0.8731 (m-30) cc_final: 0.8453 (p0) REVERT: D 17 ASP cc_start: 0.8242 (t0) cc_final: 0.7890 (t0) REVERT: D 139 TYR cc_start: 0.7686 (t80) cc_final: 0.7310 (t80) REVERT: D 197 HIS cc_start: 0.6671 (t-90) cc_final: 0.5737 (t70) REVERT: B 455 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8829 (tt0) outliers start: 37 outliers final: 14 residues processed: 114 average time/residue: 0.5258 time to fit residues: 65.6632 Evaluate side-chains 93 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 151 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN A 557 ASN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.117420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.081438 restraints weight = 27817.462| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.72 r_work: 0.3361 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13646 Z= 0.161 Angle : 0.591 7.502 18604 Z= 0.311 Chirality : 0.046 0.167 2064 Planarity : 0.005 0.048 2380 Dihedral : 5.106 54.049 1854 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.72 % Allowed : 11.11 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.21), residues: 1702 helix: -1.79 (0.72), residues: 44 sheet: -0.92 (0.18), residues: 762 loop : -0.54 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.021 0.002 TYR A 351 PHE 0.023 0.002 PHE D 138 TRP 0.014 0.002 TRP C 115 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00359 (13624) covalent geometry : angle 0.59046 (18560) SS BOND : bond 0.00347 ( 22) SS BOND : angle 0.71622 ( 44) hydrogen bonds : bond 0.03354 ( 426) hydrogen bonds : angle 6.38492 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.554 Fit side-chains REVERT: E 74 ASP cc_start: 0.8502 (t70) cc_final: 0.7791 (t0) REVERT: F 17 ASP cc_start: 0.8701 (m-30) cc_final: 0.8168 (m-30) REVERT: F 24 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7620 (mpt-90) REVERT: F 116 ILE cc_start: 0.8109 (tt) cc_final: 0.7257 (pp) REVERT: F 169 ASP cc_start: 0.8837 (p0) cc_final: 0.8373 (p0) REVERT: A 393 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7888 (pp20) REVERT: A 550 GLN cc_start: 0.8000 (tt0) cc_final: 0.7766 (tt0) REVERT: C 3 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: C 160 ASP cc_start: 0.8706 (m-30) cc_final: 0.8384 (p0) REVERT: C 211 ILE cc_start: 0.8429 (pp) cc_final: 0.8226 (tt) REVERT: D 17 ASP cc_start: 0.8255 (t0) cc_final: 0.7848 (t0) REVERT: D 139 TYR cc_start: 0.7899 (t80) cc_final: 0.7300 (t80) REVERT: D 197 HIS cc_start: 0.6843 (t-90) cc_final: 0.6004 (t70) outliers start: 26 outliers final: 3 residues processed: 113 average time/residue: 0.5053 time to fit residues: 63.3729 Evaluate side-chains 91 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 291 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 123 GLN F 136 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.116353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082393 restraints weight = 27386.489| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.75 r_work: 0.3354 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13646 Z= 0.191 Angle : 0.602 8.485 18604 Z= 0.316 Chirality : 0.046 0.176 2064 Planarity : 0.005 0.048 2380 Dihedral : 5.032 52.559 1854 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.52 % Allowed : 12.30 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.21), residues: 1702 helix: -1.68 (0.73), residues: 44 sheet: -0.86 (0.18), residues: 758 loop : -0.48 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 210 TYR 0.018 0.002 TYR B 351 PHE 0.026 0.002 PHE D 138 TRP 0.011 0.001 TRP E 48 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00438 (13624) covalent geometry : angle 0.59900 (18560) SS BOND : bond 0.00374 ( 22) SS BOND : angle 1.33796 ( 44) hydrogen bonds : bond 0.03309 ( 426) hydrogen bonds : angle 6.20088 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.522 Fit side-chains REVERT: E 74 ASP cc_start: 0.8514 (t70) cc_final: 0.7798 (t0) REVERT: F 17 ASP cc_start: 0.8687 (m-30) cc_final: 0.8191 (m-30) REVERT: F 24 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7721 (mpt-90) REVERT: F 116 ILE cc_start: 0.8107 (tt) cc_final: 0.7260 (pp) REVERT: F 169 ASP cc_start: 0.8816 (p0) cc_final: 0.8329 (p0) REVERT: A 393 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: A 455 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: A 550 GLN cc_start: 0.8013 (tt0) cc_final: 0.7770 (tt0) REVERT: C 3 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: C 160 ASP cc_start: 0.8668 (m-30) cc_final: 0.8366 (p0) REVERT: D 17 ASP cc_start: 0.8303 (t0) cc_final: 0.7888 (t0) REVERT: D 139 TYR cc_start: 0.7871 (t80) cc_final: 0.7359 (t80) REVERT: D 185 TYR cc_start: 0.7469 (t80) cc_final: 0.7132 (t80) REVERT: D 197 HIS cc_start: 0.6770 (t-90) cc_final: 0.5858 (t70) REVERT: B 455 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8675 (tt0) outliers start: 23 outliers final: 10 residues processed: 108 average time/residue: 0.5061 time to fit residues: 60.2095 Evaluate side-chains 95 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 24 optimal weight: 0.0770 chunk 167 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.117587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.083755 restraints weight = 27462.736| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.55 r_work: 0.3400 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13646 Z= 0.135 Angle : 0.580 9.205 18604 Z= 0.304 Chirality : 0.046 0.187 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.887 50.476 1854 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.19 % Allowed : 12.90 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.21), residues: 1702 helix: -1.49 (0.77), residues: 44 sheet: -0.76 (0.19), residues: 742 loop : -0.44 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 141 TYR 0.017 0.001 TYR B 351 PHE 0.027 0.001 PHE D 138 TRP 0.012 0.001 TRP C 115 HIS 0.004 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00307 (13624) covalent geometry : angle 0.57891 (18560) SS BOND : bond 0.00367 ( 22) SS BOND : angle 1.03456 ( 44) hydrogen bonds : bond 0.03033 ( 426) hydrogen bonds : angle 5.92883 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.326 Fit side-chains REVERT: E 74 ASP cc_start: 0.8473 (t70) cc_final: 0.7781 (t0) REVERT: F 17 ASP cc_start: 0.8661 (m-30) cc_final: 0.8113 (m-30) REVERT: F 24 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7697 (mpt-90) REVERT: F 116 ILE cc_start: 0.8068 (tt) cc_final: 0.7274 (pp) REVERT: F 169 ASP cc_start: 0.8765 (p0) cc_final: 0.8242 (p0) REVERT: A 393 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7911 (pp20) REVERT: A 455 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: A 550 GLN cc_start: 0.7993 (tt0) cc_final: 0.7782 (tt0) REVERT: C 3 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: C 160 ASP cc_start: 0.8609 (m-30) cc_final: 0.8302 (p0) REVERT: C 211 ILE cc_start: 0.8388 (pp) cc_final: 0.8149 (tt) REVERT: D 17 ASP cc_start: 0.8333 (t0) cc_final: 0.7909 (t0) REVERT: D 18 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8525 (ttt-90) REVERT: D 139 TYR cc_start: 0.7828 (t80) cc_final: 0.7373 (t80) REVERT: D 197 HIS cc_start: 0.6769 (t-90) cc_final: 0.5997 (t70) outliers start: 18 outliers final: 9 residues processed: 115 average time/residue: 0.4951 time to fit residues: 62.5201 Evaluate side-chains 99 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN C 5 GLN B 326 ASN B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.116770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.081170 restraints weight = 27523.601| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.74 r_work: 0.3348 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13646 Z= 0.207 Angle : 0.613 9.711 18604 Z= 0.319 Chirality : 0.047 0.179 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.895 49.039 1854 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.12 % Allowed : 13.49 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.21), residues: 1702 helix: -1.42 (0.75), residues: 44 sheet: -0.81 (0.18), residues: 756 loop : -0.41 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 141 TYR 0.015 0.002 TYR A 291 PHE 0.026 0.002 PHE D 138 TRP 0.011 0.002 TRP C 170 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00480 (13624) covalent geometry : angle 0.61192 (18560) SS BOND : bond 0.00264 ( 22) SS BOND : angle 1.00931 ( 44) hydrogen bonds : bond 0.03217 ( 426) hydrogen bonds : angle 5.93890 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.397 Fit side-chains REVERT: E 74 ASP cc_start: 0.8552 (t70) cc_final: 0.7898 (t0) REVERT: F 17 ASP cc_start: 0.8675 (m-30) cc_final: 0.8169 (m-30) REVERT: F 116 ILE cc_start: 0.8061 (tt) cc_final: 0.7292 (pp) REVERT: F 169 ASP cc_start: 0.8768 (p0) cc_final: 0.8262 (p0) REVERT: A 393 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: A 550 GLN cc_start: 0.8059 (tt0) cc_final: 0.7815 (tt0) REVERT: C 160 ASP cc_start: 0.8685 (m-30) cc_final: 0.8372 (p0) REVERT: C 211 ILE cc_start: 0.8388 (pp) cc_final: 0.8139 (tt) REVERT: D 17 ASP cc_start: 0.8337 (t0) cc_final: 0.7924 (t0) REVERT: D 139 TYR cc_start: 0.7862 (t80) cc_final: 0.7427 (t80) REVERT: D 197 HIS cc_start: 0.6966 (t-90) cc_final: 0.6344 (t70) REVERT: D 208 PHE cc_start: 0.5490 (OUTLIER) cc_final: 0.5199 (p90) REVERT: B 455 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8705 (tt0) outliers start: 17 outliers final: 8 residues processed: 105 average time/residue: 0.4950 time to fit residues: 57.1430 Evaluate side-chains 95 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 0.0060 chunk 133 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 128 optimal weight: 40.0000 chunk 44 optimal weight: 8.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.116328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.082114 restraints weight = 27466.281| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.51 r_work: 0.3370 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13646 Z= 0.179 Angle : 0.601 10.406 18604 Z= 0.313 Chirality : 0.046 0.176 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.857 47.587 1854 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.06 % Allowed : 13.89 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.21), residues: 1702 helix: -1.37 (0.75), residues: 44 sheet: -0.73 (0.19), residues: 744 loop : -0.42 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 141 TYR 0.020 0.002 TYR A 291 PHE 0.026 0.002 PHE D 138 TRP 0.012 0.001 TRP E 115 HIS 0.004 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00412 (13624) covalent geometry : angle 0.59986 (18560) SS BOND : bond 0.00269 ( 22) SS BOND : angle 0.90306 ( 44) hydrogen bonds : bond 0.03103 ( 426) hydrogen bonds : angle 5.87157 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.561 Fit side-chains REVERT: E 74 ASP cc_start: 0.8508 (t70) cc_final: 0.7856 (t0) REVERT: F 17 ASP cc_start: 0.8643 (m-30) cc_final: 0.8135 (m-30) REVERT: F 24 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7625 (mpt-90) REVERT: F 116 ILE cc_start: 0.8128 (tt) cc_final: 0.7283 (pp) REVERT: F 169 ASP cc_start: 0.8732 (p0) cc_final: 0.8203 (p0) REVERT: A 393 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7879 (pp20) REVERT: A 550 GLN cc_start: 0.8052 (tt0) cc_final: 0.7802 (tt0) REVERT: C 160 ASP cc_start: 0.8623 (m-30) cc_final: 0.8332 (p0) REVERT: D 17 ASP cc_start: 0.8369 (t0) cc_final: 0.7877 (t0) REVERT: D 18 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.8593 (ttt-90) REVERT: D 139 TYR cc_start: 0.7787 (t80) cc_final: 0.7379 (t80) REVERT: D 197 HIS cc_start: 0.6887 (t-90) cc_final: 0.6231 (t70) REVERT: D 208 PHE cc_start: 0.5499 (OUTLIER) cc_final: 0.5174 (p90) REVERT: B 455 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: B 555 ASP cc_start: 0.8856 (p0) cc_final: 0.8310 (t0) outliers start: 16 outliers final: 8 residues processed: 107 average time/residue: 0.5036 time to fit residues: 59.2856 Evaluate side-chains 99 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN B 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.116731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.080952 restraints weight = 27529.479| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.80 r_work: 0.3342 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13646 Z= 0.206 Angle : 0.622 10.064 18604 Z= 0.324 Chirality : 0.047 0.172 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.899 45.677 1854 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.93 % Allowed : 13.96 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.21), residues: 1702 helix: -1.36 (0.74), residues: 44 sheet: -0.79 (0.18), residues: 768 loop : -0.36 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.024 0.002 TYR A 291 PHE 0.024 0.002 PHE D 138 TRP 0.010 0.001 TRP C 48 HIS 0.004 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00476 (13624) covalent geometry : angle 0.62145 (18560) SS BOND : bond 0.00273 ( 22) SS BOND : angle 0.94289 ( 44) hydrogen bonds : bond 0.03197 ( 426) hydrogen bonds : angle 5.90664 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.383 Fit side-chains REVERT: F 17 ASP cc_start: 0.8630 (m-30) cc_final: 0.8115 (m-30) REVERT: F 24 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7617 (mpt-90) REVERT: F 116 ILE cc_start: 0.8118 (tt) cc_final: 0.7347 (pp) REVERT: F 169 ASP cc_start: 0.8768 (p0) cc_final: 0.8267 (p0) REVERT: A 393 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7887 (pp20) REVERT: A 550 GLN cc_start: 0.8092 (tt0) cc_final: 0.7842 (tt0) REVERT: C 160 ASP cc_start: 0.8698 (m-30) cc_final: 0.8406 (p0) REVERT: C 211 ILE cc_start: 0.8330 (pp) cc_final: 0.8029 (tt) REVERT: D 17 ASP cc_start: 0.8397 (t0) cc_final: 0.7924 (t0) REVERT: D 139 TYR cc_start: 0.7734 (t80) cc_final: 0.7307 (t80) REVERT: D 185 TYR cc_start: 0.7352 (t80) cc_final: 0.6949 (t80) REVERT: D 197 HIS cc_start: 0.6886 (t-90) cc_final: 0.6240 (t-90) REVERT: B 455 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8712 (tt0) outliers start: 14 outliers final: 7 residues processed: 101 average time/residue: 0.4932 time to fit residues: 54.9765 Evaluate side-chains 91 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 113 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN B 269 ASN B 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.116437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.082295 restraints weight = 27466.061| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.53 r_work: 0.3369 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13646 Z= 0.170 Angle : 0.608 9.561 18604 Z= 0.317 Chirality : 0.046 0.171 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.847 43.922 1854 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.86 % Allowed : 14.09 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.21), residues: 1702 helix: -1.23 (0.75), residues: 44 sheet: -0.67 (0.19), residues: 740 loop : -0.41 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 18 TYR 0.021 0.002 TYR A 291 PHE 0.027 0.002 PHE D 138 TRP 0.011 0.001 TRP E 115 HIS 0.004 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00393 (13624) covalent geometry : angle 0.60721 (18560) SS BOND : bond 0.00256 ( 22) SS BOND : angle 0.84838 ( 44) hydrogen bonds : bond 0.03068 ( 426) hydrogen bonds : angle 5.81929 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5036.16 seconds wall clock time: 86 minutes 31.17 seconds (5191.17 seconds total)