Starting phenix.real_space_refine on Thu Jul 2 12:11:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.map" model { file = "/net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b4i_15849/07_2026/8b4i_15849.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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 C 5322 2.51 5 N 1347 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 8242 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} Conformer: "B" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} bond proxies already assigned to first conformer: 2547 Chain: "B" Number of atoms: 2515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} Conformer: "B" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} bond proxies already assigned to first conformer: 2547 Chain: "C" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 450 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 450 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 290 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "F" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 290 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 289 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "H" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 289 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 408 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "J" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 408 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'DU0': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'DU0': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'DU0': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.03, per 1000 atoms: 0.25 Number of scatterers: 8242 At special positions: 0 Unit cell: (123.876, 106.299, 99.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 1 15.00 O 1548 8.00 N 1347 7.00 C 5322 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: 0.59 Conformation dependent library (CDL) restraints added in 369.1 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 38.9% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.832A pdb=" N PHE A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 334 through 343 removed outlier: 4.345A pdb=" N GLU A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 334 through 343 removed outlier: 4.344A pdb=" N GLU B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLY B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 122 Proline residue: C 99 - end of helix Processing helix chain 'D' and resid 64 through 122 Proline residue: D 99 - end of helix Processing helix chain 'E' and resid 11 through 46 Proline residue: E 40 - end of helix Processing helix chain 'F' and resid 11 through 46 Proline residue: F 40 - end of helix Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.978A pdb=" N THR G 28 " --> pdb=" O TYR G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 51 Processing helix chain 'G' and resid 52 through 58 Processing helix chain 'H' and resid 23 through 28 removed outlier: 4.072A pdb=" N THR H 28 " --> pdb=" O TYR H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 50 removed outlier: 4.727A pdb=" N VAL H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'I' and resid 5 through 39 removed outlier: 3.655A pdb=" N ARG I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU I 28 " --> pdb=" O HIS I 24 " (cutoff:3.500A) Proline residue: I 29 - end of helix Processing helix chain 'I' and resid 44 through 49 removed outlier: 3.775A pdb=" N LEU I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU I 49 " --> pdb=" O ILE I 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 44 through 49' Processing helix chain 'J' and resid 5 through 39 removed outlier: 3.552A pdb=" N ARG J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU J 28 " --> pdb=" O HIS J 24 " (cutoff:3.500A) Proline residue: J 29 - end of helix Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.922A pdb=" N LEU J 49 " --> pdb=" O ILE J 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 74 removed outlier: 6.345A pdb=" N PHE A 79 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 135 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 147 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA A 144 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 159 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A 172 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 207 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 280 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 319 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY A 64 " --> pdb=" O MET A 324 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL A 326 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 66 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE A 328 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP A 68 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA A 330 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 70 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 74 removed outlier: 6.295A pdb=" N PHE B 79 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE B 135 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA B 144 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 172 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 207 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 319 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY B 64 " --> pdb=" O MET B 324 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL B 326 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG B 66 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 328 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 68 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA B 330 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 70 " --> pdb=" O ALA B 330 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1600 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: 1.13 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1384 1.32 - 1.44: 2230 1.44 - 1.56: 4773 1.56 - 1.68: 2 1.68 - 1.80: 46 Bond restraints: 8435 Sorted by residual: bond pdb=" C22 DU0 B 402 " pdb=" O23 DU0 B 402 " ideal model delta sigma weight residual 1.412 1.439 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C22 DU0 A 401 " pdb=" O23 DU0 A 401 " ideal model delta sigma weight residual 1.412 1.437 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C09 DU0 C 201 " pdb=" O16 DU0 C 201 " ideal model delta sigma weight residual 1.404 1.429 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C09 DU0 B 402 " pdb=" O16 DU0 B 402 " ideal model delta sigma weight residual 1.404 1.428 -0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" C24 DU0 C 201 " pdb=" O23 DU0 C 201 " ideal model delta sigma weight residual 1.409 1.433 -0.024 2.00e-02 2.50e+03 1.48e+00 ... (remaining 8430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 11083 1.40 - 2.80: 318 2.80 - 4.21: 58 4.21 - 5.61: 24 5.61 - 7.01: 4 Bond angle restraints: 11487 Sorted by residual: angle pdb=" N SER A 288 " pdb=" CA SER A 288 " pdb=" C SER A 288 " ideal model delta sigma weight residual 113.28 110.33 2.95 1.22e+00 6.72e-01 5.84e+00 angle pdb=" N SER B 288 " pdb=" CA SER B 288 " pdb=" C SER B 288 " ideal model delta sigma weight residual 113.28 110.35 2.93 1.22e+00 6.72e-01 5.76e+00 angle pdb=" O10 DU0 C 201 " pdb=" C09 DU0 C 201 " pdb=" O16 DU0 C 201 " ideal model delta sigma weight residual 110.24 103.23 7.01 3.00e+00 1.11e-01 5.46e+00 angle pdb=" O10 DU0 D 201 " pdb=" C09 DU0 D 201 " pdb=" O16 DU0 D 201 " ideal model delta sigma weight residual 110.24 103.50 6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" O10 DU0 C 202 " pdb=" C09 DU0 C 202 " pdb=" O16 DU0 C 202 " ideal model delta sigma weight residual 110.24 103.85 6.39 3.00e+00 1.11e-01 4.53e+00 ... (remaining 11482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 4767 23.92 - 47.83: 79 47.83 - 71.75: 24 71.75 - 95.66: 7 95.66 - 119.58: 10 Dihedral angle restraints: 4887 sinusoidal: 1935 harmonic: 2952 Sorted by residual: dihedral pdb=" C26 DU0 B 402 " pdb=" C24 DU0 B 402 " pdb=" C25 DU0 B 402 " pdb=" O23 DU0 B 402 " ideal model delta sinusoidal sigma weight residual 189.32 69.74 119.58 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C26 DU0 A 401 " pdb=" C24 DU0 A 401 " pdb=" C25 DU0 A 401 " pdb=" O23 DU0 A 401 " ideal model delta sinusoidal sigma weight residual 189.32 72.71 116.61 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C09 DU0 C 203 " pdb=" C11 DU0 C 203 " pdb=" O10 DU0 C 203 " pdb=" C12 DU0 C 203 " ideal model delta sinusoidal sigma weight residual 58.49 -57.14 115.63 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 4884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 983 0.039 - 0.077: 256 0.077 - 0.116: 55 0.116 - 0.154: 15 0.154 - 0.193: 12 Chirality restraints: 1321 Sorted by residual: chirality pdb=" C07 DU0 C 203 " pdb=" C06 DU0 C 203 " pdb=" C08 DU0 C 203 " pdb=" C09 DU0 C 203 " both_signs ideal model delta sigma weight residual False 2.56 2.76 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" C07 DU0 D 203 " pdb=" C06 DU0 D 203 " pdb=" C08 DU0 D 203 " pdb=" C09 DU0 D 203 " both_signs ideal model delta sigma weight residual False 2.56 2.75 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" C07 DU0 A 401 " pdb=" C06 DU0 A 401 " pdb=" C08 DU0 A 401 " pdb=" C09 DU0 A 401 " both_signs ideal model delta sigma weight residual False 2.56 2.75 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1318 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 28 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO I 29 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 29 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 29 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 40 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO J 41 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 40 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 41 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.016 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1013 2.74 - 3.28: 8101 3.28 - 3.82: 12385 3.82 - 4.36: 14931 4.36 - 4.90: 27112 Nonbonded interactions: 63542 Sorted by model distance: nonbonded pdb=" O GLY I 35 " pdb=" OG SER I 39 " model vdw 2.205 3.040 nonbonded pdb=" O23 DU0 D 202 " pdb=" O52 DU0 D 202 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS A 132 " pdb=" OE1 GLU A 149 " model vdw 2.238 3.120 nonbonded pdb=" N GLN A 228 " pdb=" OE1 GLN A 228 " model vdw 2.250 3.120 nonbonded pdb=" O GLY J 35 " pdb=" OG SER J 39 " model vdw 2.271 3.040 ... (remaining 63537 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 25 through 308 or resid 310 through 349)) selection = (chain 'B' and (resid 25 through 308 or resid 310 through 349)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.00 max=1.00 mean=0.99 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: 3.500 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.130 Find NCS groups from input model: 0.110 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8435 Z= 0.210 Angle : 0.618 7.008 11487 Z= 0.310 Chirality : 0.041 0.193 1321 Planarity : 0.003 0.029 1412 Dihedral : 12.725 119.578 2987 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.24 % Allowed : 2.68 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 1008 helix: 2.10 (0.27), residues: 352 sheet: -0.41 (0.26), residues: 398 loop : -0.48 (0.46), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 37 TYR 0.007 0.001 TYR H 24 PHE 0.008 0.001 PHE A 271 TRP 0.010 0.001 TRP B 236 HIS 0.002 0.001 HIS I 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 ( 8435) covalent geometry : angle 0.61829 / 0.31 (11487) hydrogen bonds : bond 0.18956 / 12.67 ( 560) hydrogen bonds : angle 7.82458 / 5.36 ( 1600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 49 ARG cc_start: 0.8428 (ptt90) cc_final: 0.8227 (ptt-90) REVERT: A 143 MET cc_start: 0.8488 (ttp) cc_final: 0.7991 (tmm) REVERT: A 215 LYS cc_start: 0.8861 (tttt) cc_final: 0.8638 (tttm) REVERT: A 321 LYS cc_start: 0.8521 (mttt) cc_final: 0.8212 (mtmt) REVERT: A 329 GLU cc_start: 0.8222 (tt0) cc_final: 0.7891 (mt-10) REVERT: B 215 LYS cc_start: 0.8960 (tttt) cc_final: 0.8702 (tttp) REVERT: B 291 LYS cc_start: 0.8877 (tttt) cc_final: 0.8501 (tttp) REVERT: B 312 ASP cc_start: 0.7717 (t0) cc_final: 0.7177 (t0) REVERT: B 321 LYS cc_start: 0.8675 (mttt) cc_final: 0.8365 (mtpp) REVERT: B 324 MET cc_start: 0.8374 (mmm) cc_final: 0.8079 (tpp) REVERT: B 329 GLU cc_start: 0.8341 (tt0) cc_final: 0.7194 (tm-30) REVERT: D 115 GLN cc_start: 0.8667 (tp40) cc_final: 0.8434 (tp40) REVERT: E 13 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8392 (pm20) REVERT: E 27 GLN cc_start: 0.8613 (mt0) cc_final: 0.8277 (mt0) REVERT: F 13 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8269 (pm20) REVERT: H 56 MET cc_start: 0.8913 (ttp) cc_final: 0.8663 (ttt) REVERT: J 36 TYR cc_start: 0.8481 (t80) cc_final: 0.8259 (t80) outliers start: 2 outliers final: 0 residues processed: 226 average time/residue: 0.0853 time to fit residues: 25.4010 Evaluate side-chains 185 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 150 HIS A 163 ASN B 84 GLN B 145 GLN B 150 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 HIS J 24 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.122946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081782 restraints weight = 35473.600| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 5.14 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 94 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8435 Z= 0.166 Angle : 0.682 8.514 11487 Z= 0.341 Chirality : 0.043 0.167 1321 Planarity : 0.004 0.039 1412 Dihedral : 11.131 105.931 1225 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.22 % Allowed : 11.31 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.03 (0.28), residues: 1008 helix: 2.56 (0.26), residues: 358 sheet: -0.20 (0.26), residues: 402 loop : -0.43 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 120 TYR 0.018 0.002 TYR I 33 PHE 0.015 0.001 PHE A 135 TRP 0.007 0.001 TRP B 236 HIS 0.001 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 8435) covalent geometry : angle 0.68208 / 0.34 (11487) hydrogen bonds : bond 0.03957 / 2.63 ( 560) hydrogen bonds : angle 5.11113 / 3.53 ( 1600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 49 ARG cc_start: 0.8322 (ptt90) cc_final: 0.7959 (ptt-90) REVERT: A 215 LYS cc_start: 0.8828 (tttt) cc_final: 0.8434 (tttp) REVERT: A 321 LYS cc_start: 0.8447 (mttt) cc_final: 0.8124 (mtmm) REVERT: A 329 GLU cc_start: 0.8091 (tt0) cc_final: 0.7766 (mt-10) REVERT: A 346 ASN cc_start: 0.8963 (t0) cc_final: 0.8749 (t0) REVERT: B 71 LYS cc_start: 0.8308 (tttp) cc_final: 0.7849 (ttmm) REVERT: B 143 MET cc_start: 0.8251 (ttt) cc_final: 0.7815 (tmm) REVERT: B 215 LYS cc_start: 0.8917 (tttt) cc_final: 0.8679 (tttm) REVERT: B 321 LYS cc_start: 0.8566 (mttt) cc_final: 0.8223 (mtpp) REVERT: B 329 GLU cc_start: 0.8066 (tt0) cc_final: 0.7232 (tm-30) REVERT: E 27 GLN cc_start: 0.8305 (mt0) cc_final: 0.7668 (mp10) REVERT: F 13 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8257 (pm20) REVERT: F 27 GLN cc_start: 0.8264 (mt0) cc_final: 0.7718 (mp10) REVERT: H 56 MET cc_start: 0.8869 (ttp) cc_final: 0.8629 (ttt) REVERT: I 6 GLU cc_start: 0.8497 (pm20) cc_final: 0.7479 (pm20) REVERT: I 7 GLU cc_start: 0.8832 (tt0) cc_final: 0.8618 (pm20) REVERT: J 6 GLU cc_start: 0.8158 (pm20) cc_final: 0.7071 (pm20) REVERT: J 7 GLU cc_start: 0.8920 (tt0) cc_final: 0.8717 (pm20) outliers start: 10 outliers final: 5 residues processed: 180 average time/residue: 0.0854 time to fit residues: 20.6024 Evaluate side-chains 163 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.123469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079329 restraints weight = 48413.364| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 5.99 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8435 Z= 0.223 Angle : 0.681 7.735 11487 Z= 0.336 Chirality : 0.042 0.187 1321 Planarity : 0.004 0.043 1412 Dihedral : 10.756 106.701 1225 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.31 % Allowed : 12.29 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.03 (0.28), residues: 1008 helix: 2.68 (0.26), residues: 356 sheet: -0.26 (0.26), residues: 402 loop : -0.49 (0.45), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 120 TYR 0.019 0.002 TYR I 33 PHE 0.014 0.002 PHE A 135 TRP 0.010 0.001 TRP B 236 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 ( 8435) covalent geometry : angle 0.68112 / 0.34 (11487) hydrogen bonds : bond 0.03568 / 2.39 ( 560) hydrogen bonds : angle 4.74956 / 3.29 ( 1600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 215 LYS cc_start: 0.8854 (tttt) cc_final: 0.8539 (tttm) REVERT: A 321 LYS cc_start: 0.8460 (mttt) cc_final: 0.8118 (mtpp) REVERT: A 329 GLU cc_start: 0.8167 (tt0) cc_final: 0.7117 (tm-30) REVERT: B 143 MET cc_start: 0.8432 (ttt) cc_final: 0.7843 (tmm) REVERT: B 215 LYS cc_start: 0.8929 (tttt) cc_final: 0.8660 (tttm) REVERT: B 321 LYS cc_start: 0.8548 (mttt) cc_final: 0.8185 (mtpp) REVERT: B 329 GLU cc_start: 0.8186 (tt0) cc_final: 0.7298 (tm-30) REVERT: E 23 THR cc_start: 0.8713 (t) cc_final: 0.8316 (t) REVERT: E 27 GLN cc_start: 0.8294 (mt0) cc_final: 0.7681 (mp10) REVERT: F 23 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8181 (t) REVERT: F 27 GLN cc_start: 0.8288 (mt0) cc_final: 0.7765 (mp10) REVERT: H 56 MET cc_start: 0.8950 (ttp) cc_final: 0.8700 (ttt) REVERT: I 6 GLU cc_start: 0.8506 (pm20) cc_final: 0.7767 (pm20) REVERT: I 7 GLU cc_start: 0.8845 (tt0) cc_final: 0.8625 (pm20) REVERT: I 17 ASP cc_start: 0.8112 (m-30) cc_final: 0.7853 (m-30) REVERT: I 42 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8207 (mmm-85) REVERT: J 6 GLU cc_start: 0.8154 (pm20) cc_final: 0.7386 (pm20) REVERT: J 7 GLU cc_start: 0.8948 (tt0) cc_final: 0.8734 (pm20) REVERT: J 17 ASP cc_start: 0.8109 (m-30) cc_final: 0.7866 (m-30) REVERT: J 42 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8196 (mmm-85) outliers start: 19 outliers final: 8 residues processed: 173 average time/residue: 0.0741 time to fit residues: 17.7430 Evaluate side-chains 169 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.122460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081809 restraints weight = 35170.560| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 5.11 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8435 Z= 0.173 Angle : 0.648 7.096 11487 Z= 0.319 Chirality : 0.041 0.139 1321 Planarity : 0.004 0.044 1412 Dihedral : 10.454 106.242 1225 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.82 % Allowed : 13.87 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.09 (0.28), residues: 1008 helix: 2.87 (0.26), residues: 348 sheet: -0.28 (0.26), residues: 412 loop : -0.48 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 118 TYR 0.021 0.002 TYR D 68 PHE 0.012 0.001 PHE A 135 TRP 0.009 0.001 TRP B 236 HIS 0.002 0.000 HIS J 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 8435) covalent geometry : angle 0.64804 / 0.32 (11487) hydrogen bonds : bond 0.03114 / 2.09 ( 560) hydrogen bonds : angle 4.56391 / 3.17 ( 1600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 215 LYS cc_start: 0.8877 (tttt) cc_final: 0.8582 (tttm) REVERT: A 321 LYS cc_start: 0.8494 (mttt) cc_final: 0.8160 (mtpp) REVERT: A 329 GLU cc_start: 0.8095 (tt0) cc_final: 0.7023 (tm-30) REVERT: B 215 LYS cc_start: 0.8944 (tttt) cc_final: 0.8663 (tttm) REVERT: B 321 LYS cc_start: 0.8515 (mttt) cc_final: 0.8177 (mtpp) REVERT: B 329 GLU cc_start: 0.8075 (tt0) cc_final: 0.7241 (tm-30) REVERT: E 23 THR cc_start: 0.8718 (t) cc_final: 0.8135 (t) REVERT: E 27 GLN cc_start: 0.8335 (mt0) cc_final: 0.7763 (mp10) REVERT: F 23 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8171 (t) REVERT: F 27 GLN cc_start: 0.8328 (mt0) cc_final: 0.7782 (mp10) REVERT: H 56 MET cc_start: 0.8867 (ttp) cc_final: 0.8624 (ttt) REVERT: I 6 GLU cc_start: 0.8399 (pm20) cc_final: 0.7764 (pm20) REVERT: J 6 GLU cc_start: 0.8160 (pm20) cc_final: 0.7539 (pm20) REVERT: J 42 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8052 (mmm-85) outliers start: 15 outliers final: 9 residues processed: 165 average time/residue: 0.0780 time to fit residues: 17.7836 Evaluate side-chains 165 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.124917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081546 restraints weight = 40061.905| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 5.63 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8435 Z= 0.137 Angle : 0.633 7.346 11487 Z= 0.311 Chirality : 0.040 0.167 1321 Planarity : 0.004 0.040 1412 Dihedral : 10.144 105.563 1225 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.46 % Allowed : 13.63 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.19 (0.28), residues: 1008 helix: 2.83 (0.26), residues: 350 sheet: -0.22 (0.25), residues: 416 loop : -0.24 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 120 TYR 0.021 0.001 TYR C 68 PHE 0.011 0.001 PHE A 135 TRP 0.008 0.001 TRP B 195 HIS 0.001 0.000 HIS I 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8435) covalent geometry : angle 0.63324 / 0.31 (11487) hydrogen bonds : bond 0.02882 / 1.94 ( 560) hydrogen bonds : angle 4.39614 / 3.06 ( 1600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 141 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7793 (tp-100) REVERT: A 215 LYS cc_start: 0.8866 (tttt) cc_final: 0.8572 (tttm) REVERT: A 321 LYS cc_start: 0.8495 (mttt) cc_final: 0.8147 (mtpp) REVERT: A 329 GLU cc_start: 0.8070 (tt0) cc_final: 0.7028 (tm-30) REVERT: B 45 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 215 LYS cc_start: 0.8924 (tttt) cc_final: 0.8653 (tttm) REVERT: B 321 LYS cc_start: 0.8515 (mttt) cc_final: 0.8175 (mtpp) REVERT: B 329 GLU cc_start: 0.8045 (tt0) cc_final: 0.7223 (tm-30) REVERT: E 23 THR cc_start: 0.8699 (t) cc_final: 0.8166 (t) REVERT: E 27 GLN cc_start: 0.8313 (mt0) cc_final: 0.7768 (mp10) REVERT: F 23 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8188 (t) REVERT: F 27 GLN cc_start: 0.8312 (mt0) cc_final: 0.7774 (mp10) REVERT: H 56 MET cc_start: 0.8900 (ttp) cc_final: 0.8679 (ttt) REVERT: J 7 GLU cc_start: 0.8567 (pm20) cc_final: 0.8361 (pm20) REVERT: J 42 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8083 (mmm-85) outliers start: 12 outliers final: 10 residues processed: 167 average time/residue: 0.0841 time to fit residues: 19.4684 Evaluate side-chains 167 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 19 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083227 restraints weight = 35891.606| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 5.47 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8435 Z= 0.124 Angle : 0.618 7.426 11487 Z= 0.303 Chirality : 0.040 0.149 1321 Planarity : 0.004 0.035 1412 Dihedral : 9.836 104.252 1225 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.46 % Allowed : 14.84 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.28), residues: 1008 helix: 2.85 (0.26), residues: 350 sheet: -0.05 (0.25), residues: 412 loop : -0.26 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 118 TYR 0.022 0.001 TYR I 36 PHE 0.011 0.001 PHE A 135 TRP 0.008 0.001 TRP B 195 HIS 0.001 0.000 HIS I 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8435) covalent geometry : angle 0.61844 / 0.30 (11487) hydrogen bonds : bond 0.02669 / 1.80 ( 560) hydrogen bonds : angle 4.26267 / 2.98 ( 1600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 141 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7748 (tp-100) REVERT: A 215 LYS cc_start: 0.8860 (tttt) cc_final: 0.8578 (tttm) REVERT: A 321 LYS cc_start: 0.8454 (mttt) cc_final: 0.8105 (mtpp) REVERT: A 329 GLU cc_start: 0.8081 (tt0) cc_final: 0.7053 (tm-30) REVERT: B 45 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 215 LYS cc_start: 0.8925 (tttt) cc_final: 0.8672 (tttm) REVERT: B 321 LYS cc_start: 0.8477 (mttt) cc_final: 0.8128 (mtpp) REVERT: B 329 GLU cc_start: 0.8060 (tt0) cc_final: 0.7218 (tm-30) REVERT: E 23 THR cc_start: 0.8675 (t) cc_final: 0.8164 (t) REVERT: E 27 GLN cc_start: 0.8305 (mt0) cc_final: 0.7757 (mp10) REVERT: F 27 GLN cc_start: 0.8324 (mt0) cc_final: 0.7836 (mp10) REVERT: H 56 MET cc_start: 0.8890 (ttp) cc_final: 0.8679 (ttt) REVERT: I 42 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8428 (mmm-85) REVERT: J 42 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8195 (mmm-85) outliers start: 12 outliers final: 9 residues processed: 173 average time/residue: 0.0837 time to fit residues: 20.0248 Evaluate side-chains 166 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 19 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080624 restraints weight = 50256.486| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 5.80 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8435 Z= 0.221 Angle : 0.660 7.083 11487 Z= 0.327 Chirality : 0.041 0.152 1321 Planarity : 0.004 0.033 1412 Dihedral : 9.774 103.899 1225 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.82 % Allowed : 14.72 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.20 (0.28), residues: 1008 helix: 2.83 (0.26), residues: 350 sheet: -0.20 (0.25), residues: 416 loop : -0.25 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 118 TYR 0.018 0.002 TYR D 68 PHE 0.023 0.002 PHE A 85 TRP 0.010 0.001 TRP B 236 HIS 0.002 0.001 HIS J 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 ( 8435) covalent geometry : angle 0.65985 / 0.33 (11487) hydrogen bonds : bond 0.02851 / 1.93 ( 560) hydrogen bonds : angle 4.32801 / 3.03 ( 1600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 84 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: A 141 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7838 (tp-100) REVERT: A 215 LYS cc_start: 0.8890 (tttt) cc_final: 0.8597 (tttm) REVERT: A 321 LYS cc_start: 0.8446 (mttt) cc_final: 0.8098 (mtpp) REVERT: A 329 GLU cc_start: 0.8126 (tt0) cc_final: 0.7085 (tm-30) REVERT: B 45 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8115 (tm-30) REVERT: B 215 LYS cc_start: 0.8942 (tttt) cc_final: 0.8684 (tttm) REVERT: B 321 LYS cc_start: 0.8516 (mttt) cc_final: 0.8139 (mtpp) REVERT: B 329 GLU cc_start: 0.8096 (tt0) cc_final: 0.7251 (tm-30) REVERT: E 23 THR cc_start: 0.8748 (t) cc_final: 0.8179 (t) REVERT: E 27 GLN cc_start: 0.8388 (mt0) cc_final: 0.7829 (mp10) REVERT: F 27 GLN cc_start: 0.8394 (mt0) cc_final: 0.7844 (mp10) REVERT: I 42 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8377 (mmm-85) REVERT: J 42 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8249 (mmm-85) outliers start: 15 outliers final: 11 residues processed: 168 average time/residue: 0.0860 time to fit residues: 20.0152 Evaluate side-chains 168 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 19 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.083772 restraints weight = 32395.123| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.98 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8435 Z= 0.135 Angle : 0.644 7.870 11487 Z= 0.318 Chirality : 0.040 0.167 1321 Planarity : 0.004 0.035 1412 Dihedral : 9.590 101.664 1225 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.58 % Allowed : 14.84 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.30 (0.28), residues: 1008 helix: 2.85 (0.26), residues: 350 sheet: -0.12 (0.25), residues: 416 loop : -0.15 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 118 TYR 0.018 0.001 TYR C 68 PHE 0.024 0.001 PHE A 85 TRP 0.008 0.001 TRP B 236 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 8435) covalent geometry : angle 0.64403 / 0.32 (11487) hydrogen bonds : bond 0.02704 / 1.84 ( 560) hydrogen bonds : angle 4.24971 / 2.98 ( 1600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 84 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: A 215 LYS cc_start: 0.8864 (tttt) cc_final: 0.8574 (tttm) REVERT: A 321 LYS cc_start: 0.8385 (mttt) cc_final: 0.8041 (mtpp) REVERT: A 329 GLU cc_start: 0.8086 (tt0) cc_final: 0.7029 (tm-30) REVERT: B 45 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 215 LYS cc_start: 0.8931 (tttt) cc_final: 0.8660 (tttm) REVERT: B 321 LYS cc_start: 0.8460 (mttt) cc_final: 0.8082 (mtpp) REVERT: B 329 GLU cc_start: 0.8031 (tt0) cc_final: 0.7184 (tm-30) REVERT: E 23 THR cc_start: 0.8692 (t) cc_final: 0.8125 (t) REVERT: E 27 GLN cc_start: 0.8362 (mt0) cc_final: 0.7813 (mp10) REVERT: F 27 GLN cc_start: 0.8372 (mt0) cc_final: 0.7820 (mp10) REVERT: I 42 ARG cc_start: 0.8752 (mmm-85) cc_final: 0.8452 (mmm-85) REVERT: J 42 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8236 (mmm-85) outliers start: 13 outliers final: 10 residues processed: 166 average time/residue: 0.0947 time to fit residues: 21.8065 Evaluate side-chains 166 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.125374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081641 restraints weight = 42609.144| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 5.80 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8435 Z= 0.145 Angle : 0.648 7.880 11487 Z= 0.322 Chirality : 0.041 0.192 1321 Planarity : 0.004 0.037 1412 Dihedral : 9.465 101.078 1225 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.46 % Allowed : 15.21 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.42 (0.28), residues: 1008 helix: 2.83 (0.26), residues: 350 sheet: 0.01 (0.25), residues: 410 loop : -0.03 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 118 TYR 0.022 0.001 TYR D 68 PHE 0.022 0.001 PHE A 85 TRP 0.008 0.001 TRP B 195 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 8435) covalent geometry : angle 0.64792 / 0.32 (11487) hydrogen bonds : bond 0.02717 / 1.87 ( 560) hydrogen bonds : angle 4.22971 / 2.98 ( 1600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 215 LYS cc_start: 0.8844 (tttt) cc_final: 0.8539 (tttm) REVERT: A 321 LYS cc_start: 0.8447 (mttt) cc_final: 0.8087 (mtpp) REVERT: A 329 GLU cc_start: 0.8112 (tt0) cc_final: 0.7052 (tm-30) REVERT: B 45 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 215 LYS cc_start: 0.8935 (tttt) cc_final: 0.8674 (tttm) REVERT: B 321 LYS cc_start: 0.8433 (mttt) cc_final: 0.8046 (mtpp) REVERT: B 329 GLU cc_start: 0.8119 (tt0) cc_final: 0.7261 (tm-30) REVERT: E 27 GLN cc_start: 0.8341 (mt0) cc_final: 0.7791 (mp10) REVERT: F 27 GLN cc_start: 0.8351 (mt0) cc_final: 0.7807 (mp10) REVERT: I 42 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8441 (mmm-85) REVERT: J 42 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: J 47 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6845 (mtm-85) outliers start: 12 outliers final: 10 residues processed: 160 average time/residue: 0.0836 time to fit residues: 18.3898 Evaluate side-chains 160 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 19 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.124443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.083599 restraints weight = 36821.217| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 5.26 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8435 Z= 0.142 Angle : 0.647 7.871 11487 Z= 0.321 Chirality : 0.041 0.191 1321 Planarity : 0.004 0.038 1412 Dihedral : 9.306 100.574 1225 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.22 % Allowed : 15.69 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.37 (0.28), residues: 1008 helix: 2.86 (0.27), residues: 350 sheet: -0.06 (0.25), residues: 416 loop : -0.10 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 118 TYR 0.022 0.001 TYR D 68 PHE 0.012 0.001 PHE B 135 TRP 0.009 0.001 TRP B 195 HIS 0.001 0.000 HIS I 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8435) covalent geometry : angle 0.64729 / 0.32 (11487) hydrogen bonds : bond 0.02653 / 1.83 ( 560) hydrogen bonds : angle 4.21000 / 2.97 ( 1600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.310 Fit side-chains REVERT: A 45 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 84 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 215 LYS cc_start: 0.8844 (tttt) cc_final: 0.8552 (tttm) REVERT: A 321 LYS cc_start: 0.8417 (mttt) cc_final: 0.8077 (mtpp) REVERT: A 329 GLU cc_start: 0.8083 (tt0) cc_final: 0.7069 (tm-30) REVERT: B 45 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 215 LYS cc_start: 0.8922 (tttt) cc_final: 0.8628 (tttm) REVERT: B 321 LYS cc_start: 0.8475 (mttt) cc_final: 0.8096 (mtpp) REVERT: B 329 GLU cc_start: 0.8124 (tt0) cc_final: 0.7313 (tm-30) REVERT: E 27 GLN cc_start: 0.8382 (mt0) cc_final: 0.7821 (mp10) REVERT: F 27 GLN cc_start: 0.8386 (mt0) cc_final: 0.7888 (mp10) REVERT: I 42 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8478 (mmm-85) REVERT: J 42 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8277 (mmm-85) REVERT: J 47 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6840 (mtm-85) outliers start: 10 outliers final: 9 residues processed: 158 average time/residue: 0.0780 time to fit residues: 16.9588 Evaluate side-chains 161 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 19 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.0060 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.124064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083476 restraints weight = 34563.534| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 5.12 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8435 Z= 0.157 Angle : 0.662 7.909 11487 Z= 0.327 Chirality : 0.041 0.187 1321 Planarity : 0.004 0.048 1412 Dihedral : 9.246 100.683 1225 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.46 % Allowed : 15.21 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.34 (0.28), residues: 1008 helix: 2.84 (0.27), residues: 350 sheet: -0.08 (0.25), residues: 416 loop : -0.09 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 118 TYR 0.022 0.002 TYR D 68 PHE 0.017 0.001 PHE A 85 TRP 0.009 0.001 TRP B 195 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 8435) covalent geometry : angle 0.66242 / 0.33 (11487) hydrogen bonds : bond 0.02633 / 1.81 ( 560) hydrogen bonds : angle 4.21053 / 2.98 ( 1600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.10 seconds wall clock time: 30 minutes 12.22 seconds (1812.22 seconds total)