Starting phenix.real_space_refine on Thu Jul 2 07:39:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.map" model { file = "/net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sda_40350/07_2026/8sda_40350.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 K 4 8.98 5 P 7 5.49 5 S 36 5.16 5 C 4963 2.51 5 N 1117 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1825 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1823 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1744 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1749 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' K': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 1.92, per 1000 atoms: 0.26 Number of scatterers: 7414 At special positions: 0 Unit cell: (96.28, 96.28, 78.02, 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) K 4 19.00 S 36 16.00 P 7 15.00 O 1287 8.00 N 1117 7.00 C 4963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 453.8 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.709A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 4.047A pdb=" N THR A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 removed outlier: 3.682A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.569A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 323 through 350 Processing helix chain 'A' and resid 359 through 373 removed outlier: 4.173A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.694A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.567A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.521A pdb=" N LYS B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 224 through 247 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.560A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 323 through 349 removed outlier: 3.520A pdb=" N LEU B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 372 removed outlier: 4.157A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.735A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 181 through 206 removed outlier: 4.002A pdb=" N THR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 250 through 256 removed outlier: 3.596A pdb=" N GLY D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 275 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 289 through 299 Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 310 through 349 removed outlier: 4.220A pdb=" N ARG D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 372 removed outlier: 4.113A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.692A pdb=" N ALA D 402 " --> pdb=" O VAL D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 427 removed outlier: 4.368A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 224 through 247 removed outlier: 3.858A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 removed outlier: 4.013A pdb=" N PHE C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 276 removed outlier: 3.740A pdb=" N ILE C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 300 through 308 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.524A pdb=" N GLN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 349 removed outlier: 3.585A pdb=" N GLY C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 372 removed outlier: 4.116A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 403 Processing helix chain 'C' and resid 403 through 427 removed outlier: 4.594A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1107 1.30 - 1.43: 1874 1.43 - 1.56: 4478 1.56 - 1.68: 26 1.68 - 1.81: 65 Bond restraints: 7550 Sorted by residual: bond pdb=" C21 POV D 602 " pdb=" O21 POV D 602 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV A 603 " pdb=" O21 POV A 603 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV A 604 " pdb=" O21 POV A 604 " ideal model delta sigma weight residual 1.330 1.457 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 POV A 606 " pdb=" O31 POV A 606 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 POV C 603 " pdb=" O21 POV C 603 " ideal model delta sigma weight residual 1.330 1.444 -0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 7545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 9903 2.55 - 5.11: 218 5.11 - 7.66: 67 7.66 - 10.22: 32 10.22 - 12.77: 15 Bond angle restraints: 10235 Sorted by residual: angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 108.34 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" O11 POV A 602 " pdb=" P POV A 602 " pdb=" O12 POV A 602 " ideal model delta sigma weight residual 97.67 109.76 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O13 POV B 602 " pdb=" P POV B 602 " pdb=" O14 POV B 602 " ideal model delta sigma weight residual 121.11 109.07 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV D 601 " pdb=" P POV D 601 " pdb=" O12 POV D 601 " ideal model delta sigma weight residual 97.67 109.48 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 POV C 602 " pdb=" P POV C 602 " pdb=" O12 POV C 602 " ideal model delta sigma weight residual 97.67 109.43 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 4194 26.14 - 52.27: 200 52.27 - 78.41: 32 78.41 - 104.54: 7 104.54 - 130.68: 1 Dihedral angle restraints: 4434 sinusoidal: 1689 harmonic: 2745 Sorted by residual: dihedral pdb=" C3 POV A 601 " pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " pdb=" C32 POV A 601 " ideal model delta sinusoidal sigma weight residual 172.61 41.93 130.68 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CB GLU A 239 " pdb=" CG GLU A 239 " pdb=" CD GLU A 239 " pdb=" OE1 GLU A 239 " ideal model delta sinusoidal sigma weight residual 0.00 -83.23 83.23 1 3.00e+01 1.11e-03 9.41e+00 dihedral pdb=" CA GLU B 349 " pdb=" CB GLU B 349 " pdb=" CG GLU B 349 " pdb=" CD GLU B 349 " ideal model delta sinusoidal sigma weight residual 60.00 115.59 -55.59 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 4431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 996 0.051 - 0.103: 215 0.103 - 0.154: 27 0.154 - 0.205: 5 0.205 - 0.257: 2 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CG LEU D 327 " pdb=" CB LEU D 327 " pdb=" CD1 LEU D 327 " pdb=" CD2 LEU D 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU C 225 " pdb=" N LEU C 225 " pdb=" C LEU C 225 " pdb=" CB LEU C 225 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA HIS C 227 " pdb=" N HIS C 227 " pdb=" C HIS C 227 " pdb=" CB HIS C 227 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 1242 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 406 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO B 406 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO B 406 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 407 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 397 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C GLY D 397 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY D 397 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 207 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 208 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.025 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.81: 2086 2.81 - 3.39: 9155 3.39 - 3.97: 13853 3.97 - 4.56: 19809 4.56 - 5.14: 27639 Nonbonded interactions: 72542 Sorted by model distance: nonbonded pdb=" O THR B 319 " pdb=" OG SER B 323 " model vdw 2.225 3.040 nonbonded pdb=" O ILE D 407 " pdb=" ND2 ASN D 411 " model vdw 2.280 3.120 nonbonded pdb=" O TYR A 376 " pdb=" K K A 609 " model vdw 2.320 2.850 nonbonded pdb=" O THR C 372 " pdb=" OG1 THR C 373 " model vdw 2.327 3.040 nonbonded pdb=" O THR A 372 " pdb=" OG1 THR A 373 " model vdw 2.355 3.040 ... (remaining 72537 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 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or \ resid 319 through 321 or (resid 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'B' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 325 or (resid 326 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'C' and (resid 172 through 211 or resid 224 through 228 or (resid 229 thr \ ough 230 and (name N or name CA or name C or name O or name CB )) or resid 231 t \ hrough 273 or (resid 274 and (name N or name CA or name C or name O or name CB ) \ ) or resid 275 or resid 288 through 409 or (resid 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 427)) selection = (chain 'D' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 175 or (resid 176 through 177 and (name N o \ r name CA or name C or name O or name CB )) or resid 178 through 308 or (resid 3 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 310 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 through 427)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.860 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.008 0.128 7550 Z= 0.425 Angle : 1.113 12.774 10235 Z= 0.501 Chirality : 0.043 0.257 1245 Planarity : 0.005 0.045 1217 Dihedral : 15.449 130.675 2644 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.29), residues: 915 helix: 1.30 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.42 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 296 TYR 0.017 0.001 TYR C 416 PHE 0.011 0.001 PHE A 194 TRP 0.009 0.001 TRP A 172 HIS 0.004 0.001 HIS C 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.43 ( 7550) covalent geometry : angle 1.11287 / 0.50 (10235) hydrogen bonds : bond 0.15137 / 9.95 ( 569) hydrogen bonds : angle 5.78705 / 4.09 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.335 Fit side-chains REVERT: D 298 MET cc_start: 0.7594 (ttm) cc_final: 0.6911 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1086 time to fit residues: 24.2459 Evaluate side-chains 123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 309 HIS D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.157744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123286 restraints weight = 10043.284| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.99 r_work: 0.3270 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7550 Z= 0.146 Angle : 0.570 7.947 10235 Z= 0.290 Chirality : 0.039 0.136 1245 Planarity : 0.004 0.033 1217 Dihedral : 11.526 107.853 1118 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.90 % Allowed : 10.85 % Favored : 87.25 % 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: 2.38 (0.29), residues: 915 helix: 1.85 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.44 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.018 0.001 TYR D 269 PHE 0.024 0.001 PHE B 415 TRP 0.011 0.001 TRP B 251 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7550) covalent geometry : angle 0.56993 / 0.29 (10235) hydrogen bonds : bond 0.03941 / 2.57 ( 569) hydrogen bonds : angle 3.99543 / 2.88 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.278 Fit side-chains REVERT: A 418 GLU cc_start: 0.8450 (tp30) cc_final: 0.7985 (tp30) REVERT: B 322 ARG cc_start: 0.8350 (tmm-80) cc_final: 0.8072 (ttp80) REVERT: D 238 MET cc_start: 0.6560 (ttp) cc_final: 0.6206 (tmm) REVERT: D 298 MET cc_start: 0.7825 (ttm) cc_final: 0.7058 (tmm) outliers start: 14 outliers final: 8 residues processed: 162 average time/residue: 0.1027 time to fit residues: 21.5916 Evaluate side-chains 139 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119783 restraints weight = 10065.072| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.16 r_work: 0.3187 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7550 Z= 0.180 Angle : 0.562 6.677 10235 Z= 0.284 Chirality : 0.040 0.146 1245 Planarity : 0.004 0.054 1217 Dihedral : 10.541 100.174 1118 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.71 % Allowed : 13.98 % Favored : 83.31 % 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: 2.42 (0.28), residues: 915 helix: 1.89 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.46 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 322 TYR 0.013 0.001 TYR B 269 PHE 0.022 0.002 PHE B 274 TRP 0.007 0.001 TRP B 366 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 7550) covalent geometry : angle 0.56226 / 0.28 (10235) hydrogen bonds : bond 0.03738 / 2.44 ( 569) hydrogen bonds : angle 3.86119 / 2.81 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.235 Fit side-chains REVERT: A 418 GLU cc_start: 0.8460 (tp30) cc_final: 0.8171 (tp30) REVERT: D 238 MET cc_start: 0.6670 (ttp) cc_final: 0.6356 (tmm) REVERT: D 298 MET cc_start: 0.7845 (ttm) cc_final: 0.7075 (tmm) outliers start: 20 outliers final: 12 residues processed: 150 average time/residue: 0.1022 time to fit residues: 19.8879 Evaluate side-chains 140 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122925 restraints weight = 10272.812| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.55 r_work: 0.3186 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7550 Z= 0.122 Angle : 0.505 6.763 10235 Z= 0.256 Chirality : 0.038 0.124 1245 Planarity : 0.004 0.035 1217 Dihedral : 9.798 92.256 1118 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.58 % Allowed : 16.69 % Favored : 80.73 % 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: 2.66 (0.29), residues: 915 helix: 2.05 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.49 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 296 TYR 0.011 0.001 TYR B 269 PHE 0.017 0.001 PHE B 274 TRP 0.008 0.001 TRP A 365 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 7550) covalent geometry : angle 0.50544 / 0.26 (10235) hydrogen bonds : bond 0.03307 / 2.14 ( 569) hydrogen bonds : angle 3.69116 / 2.69 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.275 Fit side-chains REVERT: A 418 GLU cc_start: 0.8623 (tp30) cc_final: 0.8234 (tp30) REVERT: A 422 GLN cc_start: 0.8172 (mm110) cc_final: 0.7783 (mm110) REVERT: B 309 HIS cc_start: 0.8884 (m90) cc_final: 0.8582 (m90) REVERT: B 322 ARG cc_start: 0.8569 (tmm-80) cc_final: 0.8284 (ttp80) REVERT: B 372 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9130 (p) REVERT: D 238 MET cc_start: 0.6761 (ttp) cc_final: 0.6311 (tmm) REVERT: D 298 MET cc_start: 0.7828 (ttm) cc_final: 0.7085 (tmm) REVERT: C 185 LYS cc_start: 0.7986 (tptm) cc_final: 0.7769 (tptt) REVERT: C 238 MET cc_start: 0.7142 (tmm) cc_final: 0.6889 (tmm) REVERT: C 297 ILE cc_start: 0.8521 (mt) cc_final: 0.8146 (mt) outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 0.1027 time to fit residues: 20.7701 Evaluate side-chains 146 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121423 restraints weight = 10272.685| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.42 r_work: 0.3181 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7550 Z= 0.139 Angle : 0.521 6.810 10235 Z= 0.263 Chirality : 0.038 0.128 1245 Planarity : 0.004 0.035 1217 Dihedral : 9.433 86.830 1118 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.04 % Allowed : 18.05 % Favored : 79.92 % 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: 2.73 (0.29), residues: 915 helix: 2.10 (0.19), residues: 751 sheet: None (None), residues: 0 loop : 0.60 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 296 TYR 0.011 0.001 TYR B 269 PHE 0.019 0.001 PHE B 274 TRP 0.007 0.001 TRP B 366 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 7550) covalent geometry : angle 0.52055 / 0.26 (10235) hydrogen bonds : bond 0.03313 / 2.16 ( 569) hydrogen bonds : angle 3.67309 / 2.68 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.293 Fit side-chains REVERT: A 418 GLU cc_start: 0.8623 (tp30) cc_final: 0.8189 (tp30) REVERT: A 422 GLN cc_start: 0.8153 (mm110) cc_final: 0.7772 (mm110) REVERT: B 309 HIS cc_start: 0.8881 (m90) cc_final: 0.8621 (m90) REVERT: B 322 ARG cc_start: 0.8509 (tmm-80) cc_final: 0.8242 (ttp80) REVERT: B 372 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.9168 (p) REVERT: D 238 MET cc_start: 0.6818 (ttp) cc_final: 0.6536 (tmm) REVERT: D 298 MET cc_start: 0.7773 (ttm) cc_final: 0.7083 (tmm) REVERT: C 185 LYS cc_start: 0.7990 (tptm) cc_final: 0.7780 (tptt) REVERT: C 238 MET cc_start: 0.7190 (tmm) cc_final: 0.6936 (tmm) outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.1084 time to fit residues: 20.6378 Evaluate side-chains 144 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122832 restraints weight = 10230.183| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.40 r_work: 0.3199 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.121 Angle : 0.513 6.853 10235 Z= 0.257 Chirality : 0.038 0.124 1245 Planarity : 0.004 0.035 1217 Dihedral : 8.992 87.209 1118 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.17 % Allowed : 18.59 % Favored : 79.24 % 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 (0.29), residues: 915 helix: 2.12 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.58 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.020 0.001 PHE B 274 TRP 0.006 0.001 TRP D 365 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7550) covalent geometry : angle 0.51269 / 0.26 (10235) hydrogen bonds : bond 0.03162 / 2.06 ( 569) hydrogen bonds : angle 3.58592 / 2.61 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.331 Fit side-chains REVERT: A 418 GLU cc_start: 0.8627 (tp30) cc_final: 0.8217 (tp30) REVERT: A 422 GLN cc_start: 0.8157 (mm110) cc_final: 0.7828 (mm110) REVERT: B 309 HIS cc_start: 0.8872 (m90) cc_final: 0.8626 (m90) REVERT: B 322 ARG cc_start: 0.8433 (tmm-80) cc_final: 0.8197 (ttm-80) REVERT: B 372 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9135 (p) REVERT: D 238 MET cc_start: 0.6870 (ttp) cc_final: 0.6564 (tmm) REVERT: D 298 MET cc_start: 0.7787 (ttm) cc_final: 0.7079 (tmm) REVERT: C 185 LYS cc_start: 0.7971 (tptm) cc_final: 0.7767 (tptt) REVERT: C 238 MET cc_start: 0.7199 (tmm) cc_final: 0.6952 (tmm) REVERT: C 297 ILE cc_start: 0.8548 (mt) cc_final: 0.8168 (mt) REVERT: C 416 TYR cc_start: 0.7494 (t80) cc_final: 0.7220 (m-80) outliers start: 16 outliers final: 11 residues processed: 150 average time/residue: 0.0968 time to fit residues: 19.0264 Evaluate side-chains 143 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 0.0060 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122386 restraints weight = 10236.236| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.40 r_work: 0.3206 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7550 Z= 0.125 Angle : 0.529 8.579 10235 Z= 0.264 Chirality : 0.038 0.126 1245 Planarity : 0.004 0.034 1217 Dihedral : 8.755 84.099 1118 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.90 % Allowed : 19.13 % Favored : 78.97 % 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: 2.86 (0.29), residues: 915 helix: 2.17 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.65 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.021 0.001 PHE B 274 TRP 0.006 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 7550) covalent geometry : angle 0.52925 / 0.26 (10235) hydrogen bonds : bond 0.03160 / 2.06 ( 569) hydrogen bonds : angle 3.56424 / 2.60 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.275 Fit side-chains REVERT: A 418 GLU cc_start: 0.8644 (tp30) cc_final: 0.8157 (tp30) REVERT: A 422 GLN cc_start: 0.8165 (mm110) cc_final: 0.7822 (mm110) REVERT: B 309 HIS cc_start: 0.8884 (m90) cc_final: 0.8616 (m90) REVERT: B 322 ARG cc_start: 0.8470 (tmm-80) cc_final: 0.8261 (ttm-80) REVERT: B 372 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9150 (p) REVERT: B 415 PHE cc_start: 0.8385 (m-80) cc_final: 0.8109 (m-80) REVERT: D 238 MET cc_start: 0.6712 (ttp) cc_final: 0.6380 (tmm) REVERT: D 298 MET cc_start: 0.7836 (ttm) cc_final: 0.7054 (tmm) REVERT: C 238 MET cc_start: 0.7036 (tmm) cc_final: 0.6793 (tmm) REVERT: C 297 ILE cc_start: 0.8471 (mt) cc_final: 0.8124 (mt) REVERT: C 352 GLU cc_start: 0.8037 (pp20) cc_final: 0.7524 (pp20) outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 0.0991 time to fit residues: 18.6559 Evaluate side-chains 141 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 262 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120632 restraints weight = 10075.167| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.13 r_work: 0.3196 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7550 Z= 0.136 Angle : 0.536 8.222 10235 Z= 0.267 Chirality : 0.038 0.128 1245 Planarity : 0.004 0.034 1217 Dihedral : 8.636 84.819 1118 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.63 % Allowed : 19.27 % Favored : 79.10 % 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: 2.90 (0.29), residues: 915 helix: 2.17 (0.19), residues: 759 sheet: None (None), residues: 0 loop : 0.84 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.024 0.001 PHE B 274 TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7550) covalent geometry : angle 0.53616 / 0.27 (10235) hydrogen bonds : bond 0.03188 / 2.08 ( 569) hydrogen bonds : angle 3.57175 / 2.61 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.271 Fit side-chains REVERT: A 418 GLU cc_start: 0.8650 (tp30) cc_final: 0.8145 (tp30) REVERT: A 422 GLN cc_start: 0.8202 (mm110) cc_final: 0.7866 (mm110) REVERT: B 309 HIS cc_start: 0.8957 (m90) cc_final: 0.8656 (m90) REVERT: B 322 ARG cc_start: 0.8640 (tmm-80) cc_final: 0.8377 (ttm-80) REVERT: B 372 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.9190 (p) REVERT: B 415 PHE cc_start: 0.8543 (m-80) cc_final: 0.8220 (m-80) REVERT: D 238 MET cc_start: 0.6847 (ttp) cc_final: 0.6494 (tmm) REVERT: D 298 MET cc_start: 0.7892 (ttm) cc_final: 0.7132 (tmm) REVERT: C 238 MET cc_start: 0.7150 (tmm) cc_final: 0.6924 (tmm) REVERT: C 297 ILE cc_start: 0.8498 (mt) cc_final: 0.8160 (mt) REVERT: C 352 GLU cc_start: 0.8141 (pp20) cc_final: 0.7530 (pp20) outliers start: 12 outliers final: 9 residues processed: 142 average time/residue: 0.0953 time to fit residues: 17.7090 Evaluate side-chains 140 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119183 restraints weight = 9931.574| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.25 r_work: 0.3169 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7550 Z= 0.159 Angle : 0.560 7.897 10235 Z= 0.279 Chirality : 0.039 0.132 1245 Planarity : 0.004 0.033 1217 Dihedral : 8.780 84.827 1118 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.90 % Allowed : 20.22 % Favored : 77.88 % 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: 2.82 (0.29), residues: 915 helix: 2.10 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.90 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 296 TYR 0.011 0.001 TYR B 269 PHE 0.024 0.001 PHE B 274 TRP 0.006 0.001 TRP B 365 HIS 0.002 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 7550) covalent geometry : angle 0.56013 / 0.28 (10235) hydrogen bonds : bond 0.03301 / 2.16 ( 569) hydrogen bonds : angle 3.64126 / 2.66 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.272 Fit side-chains REVERT: A 418 GLU cc_start: 0.8595 (tp30) cc_final: 0.8052 (tp30) REVERT: A 422 GLN cc_start: 0.8196 (mm110) cc_final: 0.7804 (mm110) REVERT: B 309 HIS cc_start: 0.8901 (m90) cc_final: 0.8560 (m90) REVERT: B 372 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9196 (p) REVERT: D 238 MET cc_start: 0.6744 (ttp) cc_final: 0.6392 (tmm) REVERT: D 298 MET cc_start: 0.7860 (ttm) cc_final: 0.7113 (tmm) REVERT: C 238 MET cc_start: 0.7173 (tmm) cc_final: 0.6935 (tmm) REVERT: C 242 LEU cc_start: 0.7580 (tp) cc_final: 0.7375 (tp) REVERT: C 297 ILE cc_start: 0.8427 (mt) cc_final: 0.8095 (mt) REVERT: C 352 GLU cc_start: 0.8150 (pp20) cc_final: 0.7604 (pp20) outliers start: 14 outliers final: 11 residues processed: 136 average time/residue: 0.1085 time to fit residues: 19.0800 Evaluate side-chains 139 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120052 restraints weight = 10068.712| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.04 r_work: 0.3217 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7550 Z= 0.127 Angle : 0.543 7.817 10235 Z= 0.271 Chirality : 0.038 0.125 1245 Planarity : 0.004 0.035 1217 Dihedral : 8.579 86.247 1118 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.49 % Allowed : 20.22 % Favored : 78.29 % 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: 2.90 (0.29), residues: 915 helix: 2.16 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.89 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.008 0.001 PHE B 346 TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7550) covalent geometry : angle 0.54310 / 0.27 (10235) hydrogen bonds : bond 0.03137 / 2.05 ( 569) hydrogen bonds : angle 3.58771 / 2.62 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.353 Fit side-chains REVERT: A 418 GLU cc_start: 0.8612 (tp30) cc_final: 0.8015 (tp30) REVERT: A 422 GLN cc_start: 0.8189 (mm110) cc_final: 0.7837 (mm110) REVERT: B 274 PHE cc_start: 0.8050 (t80) cc_final: 0.7822 (t80) REVERT: B 309 HIS cc_start: 0.8944 (m90) cc_final: 0.8645 (m90) REVERT: B 372 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9196 (p) REVERT: D 238 MET cc_start: 0.6798 (ttp) cc_final: 0.6417 (tmm) REVERT: D 298 MET cc_start: 0.7881 (ttm) cc_final: 0.7151 (tmm) REVERT: C 238 MET cc_start: 0.7240 (tmm) cc_final: 0.7009 (tmm) REVERT: C 297 ILE cc_start: 0.8425 (mt) cc_final: 0.8099 (mt) REVERT: C 352 GLU cc_start: 0.8307 (pp20) cc_final: 0.7603 (pp20) outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 0.1098 time to fit residues: 19.2601 Evaluate side-chains 136 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.2980 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120113 restraints weight = 9905.099| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.31 r_work: 0.3178 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7550 Z= 0.137 Angle : 0.554 7.770 10235 Z= 0.277 Chirality : 0.038 0.143 1245 Planarity : 0.004 0.035 1217 Dihedral : 8.526 86.934 1118 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.49 % Allowed : 20.35 % Favored : 78.15 % 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: 2.88 (0.29), residues: 915 helix: 2.14 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.87 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.010 0.001 PHE A 341 TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7550) covalent geometry : angle 0.55412 / 0.28 (10235) hydrogen bonds : bond 0.03187 / 2.09 ( 569) hydrogen bonds : angle 3.61958 / 2.64 ( 1635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.70 seconds wall clock time: 33 minutes 54.28 seconds (2034.28 seconds total)