Starting phenix.real_space_refine on Tue Nov 18 12:15:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dt0_8911/11_2025/6dt0_8911.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dt0_8911/11_2025/6dt0_8911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dt0_8911/11_2025/6dt0_8911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dt0_8911/11_2025/6dt0_8911.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dt0_8911/11_2025/6dt0_8911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dt0_8911/11_2025/6dt0_8911.map" } resolution = 3.7 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 18 5.16 5 C 4688 2.51 5 N 1244 2.21 5 O 1182 1.98 5 H 6626 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13759 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3448 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 8, 'ASP:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3431 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3448 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 8, 'ASP:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3431 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.19 Number of scatterers: 13759 At special positions: 0 Unit cell: (77.05, 83.95, 139.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 18 16.00 O 1182 8.00 N 1244 7.00 C 4688 6.00 H 6626 1.00 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: 1.24 Conformation dependent library (CDL) restraints added in 492.2 milliseconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 64.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.658A pdb=" N VAL A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 288 through 349 removed outlier: 4.580A pdb=" N ARG A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG A 299 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 357 through 380 removed outlier: 3.537A pdb=" N ASN A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 407 through 432 removed outlier: 3.513A pdb=" N TRP A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 4.076A pdb=" N VAL B 168 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.597A pdb=" N PHE B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 350 removed outlier: 5.990A pdb=" N TYR B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N MET B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 356 Processing helix chain 'B' and resid 357 through 380 Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 408 through 432 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.653A pdb=" N VAL C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 288 through 349 removed outlier: 4.583A pdb=" N ARG C 292 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG C 299 " --> pdb=" O TYR C 295 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 357 through 380 removed outlier: 3.542A pdb=" N ASN C 380 " --> pdb=" O PHE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 407 through 432 removed outlier: 3.507A pdb=" N TRP C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.078A pdb=" N VAL D 168 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.595A pdb=" N PHE D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 350 removed outlier: 5.984A pdb=" N TYR D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N MET D 296 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 356 Processing helix chain 'D' and resid 357 through 380 Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 408 through 432 Processing helix chain 'D' and resid 437 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 159 removed outlier: 4.045A pdb=" N LEU A 111 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 282 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 193 Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 159 removed outlier: 4.046A pdb=" N LEU C 111 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 282 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 110 through 113 Processing sheet with id=AA6, first strand: chain 'D' and resid 190 through 193 552 hydrogen bonds defined for protein. 1590 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: 3.03 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6622 1.03 - 1.22: 6 1.22 - 1.42: 3177 1.42 - 1.61: 4117 1.61 - 1.80: 32 Bond restraints: 13954 Sorted by residual: bond pdb=" N ASN B 189 " pdb=" CA ASN B 189 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.58e+00 bond pdb=" N GLU D 276 " pdb=" CA GLU D 276 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.30e+00 bond pdb=" N ILE D 280 " pdb=" CA ILE D 280 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.20e-02 6.94e+03 5.64e+00 bond pdb=" N GLY D 277 " pdb=" CA GLY D 277 " ideal model delta sigma weight residual 1.449 1.478 -0.029 1.45e-02 4.76e+03 3.98e+00 bond pdb=" N TYR D 278 " pdb=" CA TYR D 278 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.84e+00 ... (remaining 13949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 21527 1.36 - 2.71: 2266 2.71 - 4.07: 1167 4.07 - 5.42: 75 5.42 - 6.78: 25 Bond angle restraints: 25060 Sorted by residual: angle pdb=" CA VAL D 286 " pdb=" C VAL D 286 " pdb=" N PRO D 287 " ideal model delta sigma weight residual 116.57 119.89 -3.32 9.80e-01 1.04e+00 1.15e+01 angle pdb=" CA GLU D 276 " pdb=" C GLU D 276 " pdb=" O GLU D 276 " ideal model delta sigma weight residual 120.55 117.34 3.21 1.06e+00 8.90e-01 9.17e+00 angle pdb=" N ASN D 279 " pdb=" CA ASN D 279 " pdb=" C ASN D 279 " ideal model delta sigma weight residual 111.74 107.83 3.91 1.35e+00 5.49e-01 8.37e+00 angle pdb=" C ILE D 275 " pdb=" N GLU D 276 " pdb=" CA GLU D 276 " ideal model delta sigma weight residual 120.28 124.09 -3.81 1.34e+00 5.57e-01 8.09e+00 angle pdb=" C VAL D 286 " pdb=" CA VAL D 286 " pdb=" CB VAL D 286 " ideal model delta sigma weight residual 109.33 111.93 -2.60 9.80e-01 1.04e+00 7.02e+00 ... (remaining 25055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 6225 14.97 - 29.95: 221 29.95 - 44.92: 59 44.92 - 59.90: 123 59.90 - 74.87: 8 Dihedral angle restraints: 6636 sinusoidal: 3268 harmonic: 3368 Sorted by residual: dihedral pdb=" CA PHE A 271 " pdb=" C PHE A 271 " pdb=" N ALA A 272 " pdb=" CA ALA A 272 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA PHE C 271 " pdb=" C PHE C 271 " pdb=" N ALA C 272 " pdb=" CA ALA C 272 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ILE A 159 " pdb=" C ILE A 159 " pdb=" N HIS A 160 " pdb=" CA HIS A 160 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 902 0.054 - 0.108: 176 0.108 - 0.163: 34 0.163 - 0.217: 2 0.217 - 0.271: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CA LEU D 356 " pdb=" N LEU D 356 " pdb=" C LEU D 356 " pdb=" CB LEU D 356 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LEU B 356 " pdb=" N LEU B 356 " pdb=" C LEU B 356 " pdb=" CB LEU B 356 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LEU C 356 " pdb=" N LEU C 356 " pdb=" C LEU C 356 " pdb=" CB LEU C 356 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 1113 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 376 " 0.005 2.00e-02 2.50e+03 1.38e-02 5.69e+00 pdb=" CG PHE D 376 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE D 376 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 376 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 376 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 376 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 376 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE D 376 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE D 376 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE D 376 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE D 376 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE D 376 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 376 " -0.005 2.00e-02 2.50e+03 1.33e-02 5.28e+00 pdb=" CG PHE B 376 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 376 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 376 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 376 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 376 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 376 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 376 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE B 376 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE B 376 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE B 376 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE B 376 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 436 " -0.005 2.00e-02 2.50e+03 1.02e-02 4.15e+00 pdb=" CG TRP C 436 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 436 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 436 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 436 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 436 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 436 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 436 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP C 436 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP C 436 " 0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP C 436 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 436 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP C 436 " -0.006 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 63 2.01 - 2.66: 17594 2.66 - 3.30: 37878 3.30 - 3.95: 44248 3.95 - 4.60: 70523 Nonbonded interactions: 170306 Sorted by model distance: nonbonded pdb=" O GLY C 365 " pdb=" HG1 THR C 368 " model vdw 1.359 2.450 nonbonded pdb=" O GLY A 365 " pdb=" HG1 THR A 368 " model vdw 1.360 2.450 nonbonded pdb=" HG1 THR D 114 " pdb=" O LEU D 118 " model vdw 1.381 2.450 nonbonded pdb=" HG1 THR B 114 " pdb=" O LEU B 118 " model vdw 1.382 2.450 nonbonded pdb=" O ALA A 364 " pdb=" HG1 THR A 367 " model vdw 1.475 2.450 ... (remaining 170301 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' and (resid 107 or (resid 108 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 109 or (resid 110 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name CE or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or r \ esid 111 through 311 or (resid 312 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3)) or resid 313 through 326 or (resid 327 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 328 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 414 through 430 or (resid 431 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 432 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 438 through 439 or (resid 440 through 441 and (name N or name \ CA or name C or name O or name CB or name H or name HA )))) selection = (chain 'B' and (resid 107 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 126 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or r \ esid 252 through 256 or (resid 257 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 258 through 298 or (resid 299 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3)) or resid 300 through 302 or (resid 303 and (name N or name CA or n \ ame C or name O or name CB or name CG or name H or name HA or name HB2 or name H \ B3)) or resid 304 through 399 or (resid 400 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 401 through 441)) selection = (chain 'C' and (resid 107 or (resid 108 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 109 or (resid 110 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name CE or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or r \ esid 111 through 311 or (resid 312 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3)) or resid 313 through 326 or (resid 327 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 328 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 414 through 430 or (resid 431 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 432 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 438 through 439 or (resid 440 through 441 and (name N or name \ CA or name C or name O or name CB or name H or name HA )))) selection = (chain 'D' and (resid 107 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 126 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or r \ esid 252 through 256 or (resid 257 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 258 through 298 or (resid 299 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3)) or resid 300 through 302 or (resid 303 and (name N or name CA or n \ ame C or name O or name CB or name CG or name H or name HA or name HB2 or name H \ B3)) or resid 304 through 399 or (resid 400 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 401 through 441)) } 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: 1.480 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.170 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.005 0.049 7328 Z= 0.252 Angle : 0.716 6.775 9992 Z= 0.396 Chirality : 0.044 0.271 1116 Planarity : 0.005 0.038 1240 Dihedral : 8.500 74.874 2444 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.45 (0.26), residues: 904 helix: -0.03 (0.20), residues: 540 sheet: -2.26 (0.36), residues: 136 loop : -2.04 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.017 0.002 TYR D 373 PHE 0.022 0.002 PHE D 376 TRP 0.024 0.002 TRP A 436 HIS 0.006 0.002 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 7328) covalent geometry : angle 0.71594 ( 9992) hydrogen bonds : bond 0.12501 ( 552) hydrogen bonds : angle 6.02086 ( 1590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.8215 (m-40) cc_final: 0.7959 (p0) REVERT: A 318 ASP cc_start: 0.8516 (m-30) cc_final: 0.8264 (m-30) REVERT: B 116 THR cc_start: 0.8874 (p) cc_final: 0.8434 (t) REVERT: B 125 LEU cc_start: 0.8898 (tp) cc_final: 0.8666 (tt) REVERT: B 173 GLN cc_start: 0.8759 (mt0) cc_final: 0.8505 (mt0) REVERT: C 189 ASN cc_start: 0.8190 (m-40) cc_final: 0.7922 (p0) REVERT: C 318 ASP cc_start: 0.8530 (m-30) cc_final: 0.8278 (m-30) REVERT: D 116 THR cc_start: 0.8880 (p) cc_final: 0.8418 (t) REVERT: D 125 LEU cc_start: 0.8992 (tp) cc_final: 0.8762 (tt) REVERT: D 173 GLN cc_start: 0.8750 (mt0) cc_final: 0.8491 (mt0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2699 time to fit residues: 80.5247 Evaluate side-chains 142 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS C 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089979 restraints weight = 56244.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093224 restraints weight = 20983.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095258 restraints weight = 10959.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096352 restraints weight = 7183.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097165 restraints weight = 5662.400| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7328 Z= 0.134 Angle : 0.530 4.627 9992 Z= 0.281 Chirality : 0.039 0.152 1116 Planarity : 0.005 0.063 1240 Dihedral : 3.915 13.609 1024 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.61 % Allowed : 7.56 % Favored : 90.84 % 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: 1.01 (0.29), residues: 904 helix: 2.00 (0.22), residues: 560 sheet: -1.66 (0.38), residues: 138 loop : -1.29 (0.47), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 440 TYR 0.014 0.001 TYR B 373 PHE 0.009 0.001 PHE C 348 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7328) covalent geometry : angle 0.53023 ( 9992) hydrogen bonds : bond 0.05282 ( 552) hydrogen bonds : angle 4.58136 ( 1590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.8276 (m-40) cc_final: 0.7907 (p0) REVERT: A 318 ASP cc_start: 0.8525 (m-30) cc_final: 0.8265 (m-30) REVERT: B 125 LEU cc_start: 0.8857 (tp) cc_final: 0.8635 (tt) REVERT: C 189 ASN cc_start: 0.8266 (m-40) cc_final: 0.7912 (p0) REVERT: C 318 ASP cc_start: 0.8595 (m-30) cc_final: 0.8287 (m-30) REVERT: D 125 LEU cc_start: 0.8927 (tp) cc_final: 0.8692 (tt) REVERT: D 282 MET cc_start: 0.8261 (ttp) cc_final: 0.8052 (ttp) outliers start: 10 outliers final: 9 residues processed: 156 average time/residue: 0.1723 time to fit residues: 36.3913 Evaluate side-chains 139 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 HIS D 326 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.084515 restraints weight = 56794.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087498 restraints weight = 21825.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.089379 restraints weight = 11741.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090417 restraints weight = 7804.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091095 restraints weight = 6137.196| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7328 Z= 0.192 Angle : 0.549 5.049 9992 Z= 0.297 Chirality : 0.039 0.146 1116 Planarity : 0.004 0.022 1240 Dihedral : 3.778 15.083 1024 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.05 % Allowed : 7.23 % Favored : 89.71 % 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: 1.92 (0.29), residues: 904 helix: 2.73 (0.22), residues: 560 sheet: -1.29 (0.38), residues: 140 loop : -1.05 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 170 TYR 0.015 0.001 TYR B 373 PHE 0.016 0.002 PHE A 348 TRP 0.013 0.001 TRP B 436 HIS 0.007 0.002 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7328) covalent geometry : angle 0.54937 ( 9992) hydrogen bonds : bond 0.05166 ( 552) hydrogen bonds : angle 4.29011 ( 1590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.8383 (m-40) cc_final: 0.7964 (p0) REVERT: A 318 ASP cc_start: 0.8383 (m-30) cc_final: 0.8067 (m-30) REVERT: A 373 TYR cc_start: 0.7866 (t80) cc_final: 0.7594 (t80) REVERT: C 189 ASN cc_start: 0.8349 (m-40) cc_final: 0.7931 (p0) REVERT: C 318 ASP cc_start: 0.8382 (m-30) cc_final: 0.8068 (m-30) REVERT: D 282 MET cc_start: 0.8328 (ttp) cc_final: 0.8073 (ttp) outliers start: 19 outliers final: 15 residues processed: 152 average time/residue: 0.1537 time to fit residues: 32.6339 Evaluate side-chains 131 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN C 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.098797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081472 restraints weight = 57267.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.084274 restraints weight = 22467.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086035 restraints weight = 12369.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087033 restraints weight = 8446.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087639 restraints weight = 6740.251| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 7328 Z= 0.207 Angle : 0.533 4.407 9992 Z= 0.291 Chirality : 0.039 0.134 1116 Planarity : 0.003 0.030 1240 Dihedral : 3.669 14.523 1024 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.86 % Allowed : 8.04 % Favored : 88.10 % 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: 2.23 (0.29), residues: 904 helix: 2.92 (0.22), residues: 562 sheet: -0.96 (0.40), residues: 140 loop : -0.95 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 423 TYR 0.011 0.001 TYR D 373 PHE 0.016 0.002 PHE A 376 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7328) covalent geometry : angle 0.53341 ( 9992) hydrogen bonds : bond 0.05038 ( 552) hydrogen bonds : angle 4.24264 ( 1590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.8360 (m-40) cc_final: 0.7875 (p0) REVERT: A 318 ASP cc_start: 0.8262 (m-30) cc_final: 0.7950 (m-30) REVERT: A 373 TYR cc_start: 0.7966 (t80) cc_final: 0.7607 (t80) REVERT: C 189 ASN cc_start: 0.8336 (m-40) cc_final: 0.7899 (p0) REVERT: C 318 ASP cc_start: 0.8270 (m-30) cc_final: 0.7956 (m-30) REVERT: C 373 TYR cc_start: 0.7983 (t80) cc_final: 0.7680 (t80) REVERT: D 282 MET cc_start: 0.8269 (ttp) cc_final: 0.8025 (ttp) outliers start: 24 outliers final: 15 residues processed: 146 average time/residue: 0.1928 time to fit residues: 37.1221 Evaluate side-chains 127 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.099476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.082155 restraints weight = 57170.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.085029 restraints weight = 22165.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086800 restraints weight = 12101.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087725 restraints weight = 8222.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088447 restraints weight = 6628.313| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7328 Z= 0.138 Angle : 0.492 4.714 9992 Z= 0.259 Chirality : 0.038 0.136 1116 Planarity : 0.003 0.031 1240 Dihedral : 3.480 12.360 1024 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.89 % Allowed : 10.29 % Favored : 86.82 % 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: 2.76 (0.30), residues: 904 helix: 3.29 (0.22), residues: 562 sheet: -0.73 (0.41), residues: 140 loop : -0.60 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 170 TYR 0.010 0.001 TYR D 373 PHE 0.013 0.001 PHE C 376 TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7328) covalent geometry : angle 0.49208 ( 9992) hydrogen bonds : bond 0.04834 ( 552) hydrogen bonds : angle 3.99535 ( 1590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.8379 (m-40) cc_final: 0.7853 (p0) REVERT: A 318 ASP cc_start: 0.8279 (m-30) cc_final: 0.7980 (m-30) REVERT: A 345 TYR cc_start: 0.8585 (t80) cc_final: 0.8172 (t80) REVERT: A 373 TYR cc_start: 0.7947 (t80) cc_final: 0.7558 (t80) REVERT: C 189 ASN cc_start: 0.8351 (m-40) cc_final: 0.7844 (p0) REVERT: C 318 ASP cc_start: 0.8283 (m-30) cc_final: 0.7983 (m-30) REVERT: C 345 TYR cc_start: 0.8594 (t80) cc_final: 0.8185 (t80) REVERT: C 373 TYR cc_start: 0.7959 (t80) cc_final: 0.7593 (t80) REVERT: D 282 MET cc_start: 0.8268 (ttp) cc_final: 0.8050 (ttp) outliers start: 18 outliers final: 12 residues processed: 146 average time/residue: 0.1543 time to fit residues: 31.9458 Evaluate side-chains 137 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.097546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.079953 restraints weight = 57192.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082850 restraints weight = 21377.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084713 restraints weight = 11616.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085676 restraints weight = 7843.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086215 restraints weight = 6338.576| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7328 Z= 0.179 Angle : 0.519 4.343 9992 Z= 0.277 Chirality : 0.038 0.132 1116 Planarity : 0.003 0.041 1240 Dihedral : 3.630 15.151 1024 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.05 % Allowed : 10.29 % Favored : 86.66 % 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: 2.78 (0.30), residues: 904 helix: 3.30 (0.22), residues: 566 sheet: -0.68 (0.41), residues: 140 loop : -0.73 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.010 0.001 TYR D 373 PHE 0.014 0.001 PHE A 348 TRP 0.006 0.001 TRP A 436 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7328) covalent geometry : angle 0.51850 ( 9992) hydrogen bonds : bond 0.04874 ( 552) hydrogen bonds : angle 4.02183 ( 1590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASP cc_start: 0.8289 (m-30) cc_final: 0.7986 (m-30) REVERT: A 340 TRP cc_start: 0.8859 (t60) cc_final: 0.8534 (t60) REVERT: A 345 TYR cc_start: 0.8715 (t80) cc_final: 0.8337 (t80) REVERT: C 318 ASP cc_start: 0.8290 (m-30) cc_final: 0.7988 (m-30) REVERT: C 340 TRP cc_start: 0.8858 (t60) cc_final: 0.8532 (t60) REVERT: C 345 TYR cc_start: 0.8719 (t80) cc_final: 0.8346 (t80) REVERT: C 373 TYR cc_start: 0.7888 (t80) cc_final: 0.7481 (t80) REVERT: D 282 MET cc_start: 0.8474 (ttp) cc_final: 0.8234 (ttp) outliers start: 19 outliers final: 14 residues processed: 137 average time/residue: 0.1572 time to fit residues: 30.1216 Evaluate side-chains 132 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.098676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081354 restraints weight = 57038.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084240 restraints weight = 21494.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086072 restraints weight = 11574.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087092 restraints weight = 7752.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087796 restraints weight = 6141.161| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7328 Z= 0.135 Angle : 0.486 4.363 9992 Z= 0.256 Chirality : 0.038 0.137 1116 Planarity : 0.003 0.023 1240 Dihedral : 3.441 13.769 1024 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.89 % Allowed : 10.61 % Favored : 86.50 % 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: 3.09 (0.29), residues: 904 helix: 3.52 (0.21), residues: 564 sheet: -0.53 (0.41), residues: 140 loop : -0.51 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.007 0.001 TYR D 373 PHE 0.013 0.001 PHE A 376 TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7328) covalent geometry : angle 0.48650 ( 9992) hydrogen bonds : bond 0.04689 ( 552) hydrogen bonds : angle 3.84576 ( 1590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASP cc_start: 0.8145 (m-30) cc_final: 0.7821 (m-30) REVERT: A 340 TRP cc_start: 0.8889 (t60) cc_final: 0.8547 (t60) REVERT: A 345 TYR cc_start: 0.8675 (t80) cc_final: 0.8314 (t80) REVERT: C 318 ASP cc_start: 0.8143 (m-30) cc_final: 0.7821 (m-30) REVERT: C 340 TRP cc_start: 0.8891 (t60) cc_final: 0.8542 (t60) REVERT: C 345 TYR cc_start: 0.8676 (t80) cc_final: 0.8317 (t80) REVERT: D 282 MET cc_start: 0.8301 (ttp) cc_final: 0.8085 (ttp) outliers start: 18 outliers final: 13 residues processed: 143 average time/residue: 0.1551 time to fit residues: 31.0765 Evaluate side-chains 138 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.098851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.081389 restraints weight = 57267.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084330 restraints weight = 21198.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086152 restraints weight = 11281.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087179 restraints weight = 7559.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087887 restraints weight = 5987.055| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7328 Z= 0.135 Angle : 0.487 4.410 9992 Z= 0.258 Chirality : 0.038 0.135 1116 Planarity : 0.003 0.022 1240 Dihedral : 3.388 14.293 1024 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.05 % Allowed : 12.06 % Favored : 84.89 % 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: 3.23 (0.30), residues: 904 helix: 3.60 (0.21), residues: 566 sheet: -0.75 (0.40), residues: 156 loop : -0.05 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.007 0.001 TYR D 373 PHE 0.013 0.001 PHE C 348 TRP 0.006 0.001 TRP A 436 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7328) covalent geometry : angle 0.48723 ( 9992) hydrogen bonds : bond 0.04624 ( 552) hydrogen bonds : angle 3.79396 ( 1590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASP cc_start: 0.8171 (m-30) cc_final: 0.7840 (m-30) REVERT: A 340 TRP cc_start: 0.8891 (t60) cc_final: 0.8548 (t60) REVERT: A 345 TYR cc_start: 0.8706 (t80) cc_final: 0.8363 (t80) REVERT: C 318 ASP cc_start: 0.8173 (m-30) cc_final: 0.7844 (m-30) REVERT: C 340 TRP cc_start: 0.8887 (t60) cc_final: 0.8536 (t60) REVERT: C 345 TYR cc_start: 0.8708 (t80) cc_final: 0.8367 (t80) REVERT: D 282 MET cc_start: 0.8373 (ttp) cc_final: 0.8128 (ttp) outliers start: 19 outliers final: 14 residues processed: 142 average time/residue: 0.1555 time to fit residues: 30.9513 Evaluate side-chains 133 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.080853 restraints weight = 57936.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.083646 restraints weight = 22165.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085380 restraints weight = 11978.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086246 restraints weight = 8082.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086895 restraints weight = 6518.611| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7328 Z= 0.186 Angle : 0.521 4.408 9992 Z= 0.279 Chirality : 0.038 0.132 1116 Planarity : 0.003 0.029 1240 Dihedral : 3.465 14.353 1024 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.22 % Allowed : 11.90 % Favored : 84.89 % 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: 3.22 (0.29), residues: 904 helix: 3.53 (0.21), residues: 566 sheet: -0.34 (0.43), residues: 140 loop : -0.32 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.009 0.001 TYR D 373 PHE 0.016 0.001 PHE C 348 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7328) covalent geometry : angle 0.52053 ( 9992) hydrogen bonds : bond 0.04804 ( 552) hydrogen bonds : angle 3.90677 ( 1590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASP cc_start: 0.8183 (m-30) cc_final: 0.7874 (m-30) REVERT: A 340 TRP cc_start: 0.8970 (t60) cc_final: 0.8572 (t60) REVERT: A 345 TYR cc_start: 0.8690 (t80) cc_final: 0.8351 (t80) REVERT: C 318 ASP cc_start: 0.8186 (m-30) cc_final: 0.7873 (m-30) REVERT: C 340 TRP cc_start: 0.8968 (t60) cc_final: 0.8561 (t60) REVERT: C 345 TYR cc_start: 0.8639 (t80) cc_final: 0.8307 (t80) outliers start: 20 outliers final: 16 residues processed: 135 average time/residue: 0.1530 time to fit residues: 29.2823 Evaluate side-chains 131 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN B 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079217 restraints weight = 57803.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082057 restraints weight = 21433.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.083704 restraints weight = 11441.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084832 restraints weight = 7841.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.085295 restraints weight = 6084.601| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7328 Z= 0.225 Angle : 0.551 4.489 9992 Z= 0.300 Chirality : 0.039 0.130 1116 Planarity : 0.004 0.023 1240 Dihedral : 3.647 14.623 1024 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.41 % Allowed : 12.86 % Favored : 84.73 % 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: 3.07 (0.29), residues: 904 helix: 3.31 (0.21), residues: 568 sheet: -0.25 (0.43), residues: 138 loop : -0.18 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.010 0.001 TYR B 373 PHE 0.016 0.002 PHE C 348 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7328) covalent geometry : angle 0.55110 ( 9992) hydrogen bonds : bond 0.05008 ( 552) hydrogen bonds : angle 4.09156 ( 1590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASP cc_start: 0.8117 (m-30) cc_final: 0.7805 (m-30) REVERT: A 340 TRP cc_start: 0.9043 (t60) cc_final: 0.8670 (t60) REVERT: A 345 TYR cc_start: 0.8742 (t80) cc_final: 0.8420 (t80) REVERT: B 306 GLU cc_start: 0.8625 (tt0) cc_final: 0.8416 (tt0) REVERT: C 318 ASP cc_start: 0.8117 (m-30) cc_final: 0.7804 (m-30) REVERT: C 340 TRP cc_start: 0.9040 (t60) cc_final: 0.8669 (t60) REVERT: C 345 TYR cc_start: 0.8744 (t80) cc_final: 0.8419 (t80) REVERT: D 306 GLU cc_start: 0.8603 (tt0) cc_final: 0.8395 (tt0) outliers start: 15 outliers final: 13 residues processed: 123 average time/residue: 0.1584 time to fit residues: 27.4124 Evaluate side-chains 122 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.096451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079097 restraints weight = 58327.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081828 restraints weight = 22374.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083517 restraints weight = 12266.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084359 restraints weight = 8401.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085142 restraints weight = 6851.684| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7328 Z= 0.191 Angle : 0.529 4.390 9992 Z= 0.284 Chirality : 0.038 0.134 1116 Planarity : 0.003 0.022 1240 Dihedral : 3.560 14.913 1024 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.25 % Allowed : 12.86 % Favored : 84.89 % 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: 3.21 (0.29), residues: 904 helix: 3.35 (0.21), residues: 572 sheet: -0.18 (0.44), residues: 138 loop : 0.02 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.010 0.001 TYR B 373 PHE 0.014 0.001 PHE C 348 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7328) covalent geometry : angle 0.52889 ( 9992) hydrogen bonds : bond 0.04884 ( 552) hydrogen bonds : angle 3.99501 ( 1590) =============================================================================== Job complete usr+sys time: 2302.88 seconds wall clock time: 39 minutes 55.25 seconds (2395.25 seconds total)