Starting phenix.real_space_refine on Tue Mar 3 18:28:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukf_26579/03_2026/7ukf_26579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukf_26579/03_2026/7ukf_26579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2026/7ukf_26579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2026/7ukf_26579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2026/7ukf_26579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2026/7ukf_26579.map" } resolution = 3.02 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= 0.005 sd= 0.068 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 Hg 1 10.96 5 K 4 8.98 5 S 60 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8005 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' HG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1842 SG CYS A 406 56.243 52.488 57.734 1.00 69.40 S Time building chain proxies: 1.83, per 1000 atoms: 0.23 Number of scatterers: 8005 At special positions: 0 Unit cell: (113.162, 112.336, 84.252, 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) Hg 1 79.96 K 4 19.00 S 60 16.00 O 1356 8.00 N 1332 7.00 C 5252 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: 0.72 Conformation dependent library (CDL) restraints added in 286.2 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.602A pdb=" N SER A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 347 removed outlier: 5.088A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 206 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 293 removed outlier: 4.021A pdb=" N VAL B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL C 290 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.973A pdb=" N PHE C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL D 290 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1767 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: 1.20 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2440 1.34 - 1.46: 1907 1.46 - 1.58: 3757 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8196 Sorted by residual: bond pdb=" C VAL B 377 " pdb=" N PRO B 378 " ideal model delta sigma weight residual 1.333 1.320 0.013 1.17e-02 7.31e+03 1.22e+00 bond pdb=" C VAL A 377 " pdb=" N PRO A 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" C VAL C 377 " pdb=" N PRO C 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" C VAL D 377 " pdb=" N PRO D 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.38e-01 ... (remaining 8191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 10563 1.22 - 2.45: 451 2.45 - 3.67: 90 3.67 - 4.89: 20 4.89 - 6.12: 12 Bond angle restraints: 11136 Sorted by residual: angle pdb=" N LEU C 400 " pdb=" CA LEU C 400 " pdb=" C LEU C 400 " ideal model delta sigma weight residual 109.81 115.30 -5.49 2.21e+00 2.05e-01 6.17e+00 angle pdb=" N LEU D 400 " pdb=" CA LEU D 400 " pdb=" C LEU D 400 " ideal model delta sigma weight residual 109.81 115.27 -5.46 2.21e+00 2.05e-01 6.11e+00 angle pdb=" N LEU A 400 " pdb=" CA LEU A 400 " pdb=" C LEU A 400 " ideal model delta sigma weight residual 109.81 115.26 -5.45 2.21e+00 2.05e-01 6.07e+00 angle pdb=" N LEU B 400 " pdb=" CA LEU B 400 " pdb=" C LEU B 400 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.03e+00 angle pdb=" CA LEU C 271 " pdb=" C LEU C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 118.44 121.56 -3.12 1.59e+00 3.96e-01 3.85e+00 ... (remaining 11131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.14: 4010 10.14 - 20.28: 530 20.28 - 30.43: 176 30.43 - 40.57: 76 40.57 - 50.71: 12 Dihedral angle restraints: 4804 sinusoidal: 1772 harmonic: 3032 Sorted by residual: dihedral pdb=" CB MET D 333 " pdb=" CG MET D 333 " pdb=" SD MET D 333 " pdb=" CE MET D 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.71 -50.71 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET A 333 " pdb=" CG MET A 333 " pdb=" SD MET A 333 " pdb=" CE MET A 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.68 -50.68 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET B 333 " pdb=" CG MET B 333 " pdb=" SD MET B 333 " pdb=" CE MET B 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.66 -50.66 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 629 0.026 - 0.051: 416 0.051 - 0.077: 183 0.077 - 0.102: 71 0.102 - 0.128: 17 Chirality restraints: 1316 Sorted by residual: chirality pdb=" CA VAL B 207 " pdb=" N VAL B 207 " pdb=" C VAL B 207 " pdb=" CB VAL B 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA VAL C 207 " pdb=" N VAL C 207 " pdb=" C VAL C 207 " pdb=" CB VAL C 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1313 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 357 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO C 358 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO D 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO B 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.025 5.00e-02 4.00e+02 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 2973 2.86 - 3.43: 9594 3.43 - 4.00: 14762 4.00 - 4.57: 21588 4.57 - 5.14: 30209 Nonbonded interactions: 79126 Sorted by model distance: nonbonded pdb=" OG1 THR B 166 " pdb=" OE1 GLN B 169 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR D 166 " pdb=" OE1 GLN D 169 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 166 " pdb=" OE1 GLN A 169 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR C 166 " pdb=" OE1 GLN C 169 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR D 188 " pdb=" O PHE D 303 " model vdw 2.339 3.040 ... (remaining 79121 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 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.031 8196 Z= 0.183 Angle : 0.611 6.115 11136 Z= 0.349 Chirality : 0.041 0.128 1316 Planarity : 0.005 0.045 1364 Dihedral : 11.495 50.711 2852 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.27), residues: 1028 helix: 0.91 (0.18), residues: 796 sheet: None (None), residues: 0 loop : 0.83 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 299 TYR 0.017 0.002 TYR C 188 PHE 0.010 0.001 PHE C 326 TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8196) covalent geometry : angle 0.61085 (11136) hydrogen bonds : bond 0.09225 ( 601) hydrogen bonds : angle 5.31653 ( 1767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0957 time to fit residues: 15.8589 Evaluate side-chains 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN B 408 ASN C 408 ASN D 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.215178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152927 restraints weight = 5703.310| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.81 r_work: 0.3328 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8196 Z= 0.196 Angle : 0.576 6.223 11136 Z= 0.301 Chirality : 0.041 0.130 1316 Planarity : 0.005 0.046 1364 Dihedral : 3.827 13.264 1148 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.35 % Allowed : 6.01 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1028 helix: 0.83 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.13 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.018 0.002 TYR A 225 PHE 0.011 0.001 PHE D 326 TRP 0.007 0.002 TRP C 172 HIS 0.002 0.000 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 8196) covalent geometry : angle 0.57640 (11136) hydrogen bonds : bond 0.05101 ( 601) hydrogen bonds : angle 4.38066 ( 1767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.299 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 108 average time/residue: 0.0894 time to fit residues: 13.3100 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.215363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152472 restraints weight = 5850.544| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.78 r_work: 0.3326 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8196 Z= 0.146 Angle : 0.521 5.971 11136 Z= 0.273 Chirality : 0.039 0.132 1316 Planarity : 0.005 0.046 1364 Dihedral : 3.623 12.765 1148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % 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: 1.29 (0.26), residues: 1028 helix: 1.13 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.06 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.017 0.001 TYR A 188 PHE 0.011 0.001 PHE D 326 TRP 0.007 0.001 TRP D 172 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8196) covalent geometry : angle 0.52149 (11136) hydrogen bonds : bond 0.04597 ( 601) hydrogen bonds : angle 4.11938 ( 1767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.205 Fit side-chains REVERT: A 257 PHE cc_start: 0.6589 (t80) cc_final: 0.6330 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0705 time to fit residues: 11.7094 Evaluate side-chains 105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.215589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157429 restraints weight = 6314.609| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.80 r_work: 0.3345 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8196 Z= 0.136 Angle : 0.508 5.715 11136 Z= 0.265 Chirality : 0.038 0.132 1316 Planarity : 0.005 0.045 1364 Dihedral : 3.514 12.386 1148 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.12 % Allowed : 10.97 % Favored : 88.92 % 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: 2.13 (0.26), residues: 1028 helix: 1.68 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.74 (0.45), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 305 TYR 0.021 0.001 TYR C 273 PHE 0.011 0.001 PHE D 326 TRP 0.007 0.001 TRP D 172 HIS 0.001 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8196) covalent geometry : angle 0.50812 (11136) hydrogen bonds : bond 0.04472 ( 601) hydrogen bonds : angle 3.99897 ( 1767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.313 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.0695 time to fit residues: 11.5633 Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.215509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154074 restraints weight = 6545.358| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.93 r_work: 0.3333 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8196 Z= 0.137 Angle : 0.507 5.477 11136 Z= 0.264 Chirality : 0.038 0.132 1316 Planarity : 0.004 0.045 1364 Dihedral : 3.482 12.093 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.24 % Allowed : 11.79 % Favored : 87.97 % 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: 2.26 (0.26), residues: 1028 helix: 1.82 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.59 (0.45), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 305 TYR 0.016 0.001 TYR A 188 PHE 0.011 0.001 PHE B 257 TRP 0.006 0.001 TRP D 172 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8196) covalent geometry : angle 0.50707 (11136) hydrogen bonds : bond 0.04428 ( 601) hydrogen bonds : angle 3.93369 ( 1767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.298 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 117 average time/residue: 0.0685 time to fit residues: 11.8018 Evaluate side-chains 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.212455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164716 restraints weight = 6749.776| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.16 r_work: 0.3293 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8196 Z= 0.216 Angle : 0.567 5.514 11136 Z= 0.298 Chirality : 0.042 0.130 1316 Planarity : 0.005 0.044 1364 Dihedral : 3.657 12.203 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.30 % Allowed : 11.56 % Favored : 87.15 % 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: 1.45 (0.26), residues: 1028 helix: 1.26 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.09 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.014 0.002 TYR A 188 PHE 0.011 0.002 PHE C 298 TRP 0.007 0.002 TRP A 362 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8196) covalent geometry : angle 0.56668 (11136) hydrogen bonds : bond 0.05130 ( 601) hydrogen bonds : angle 4.14338 ( 1767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.290 Fit side-chains REVERT: C 411 ARG cc_start: 0.8433 (tmm-80) cc_final: 0.8143 (tmm-80) REVERT: D 411 ARG cc_start: 0.8424 (tmm-80) cc_final: 0.8217 (tmm-80) outliers start: 11 outliers final: 11 residues processed: 118 average time/residue: 0.0843 time to fit residues: 13.9782 Evaluate side-chains 121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.214189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167846 restraints weight = 6890.370| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.19 r_work: 0.3312 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8196 Z= 0.153 Angle : 0.522 5.253 11136 Z= 0.272 Chirality : 0.039 0.133 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.561 12.419 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 13.68 % Favored : 85.38 % 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: 1.67 (0.26), residues: 1028 helix: 1.41 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.02 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 305 TYR 0.016 0.001 TYR A 188 PHE 0.013 0.001 PHE B 257 TRP 0.007 0.001 TRP A 172 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8196) covalent geometry : angle 0.52187 (11136) hydrogen bonds : bond 0.04607 ( 601) hydrogen bonds : angle 4.00886 ( 1767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.229 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 121 average time/residue: 0.0757 time to fit residues: 13.0490 Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 76 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.214411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.165263 restraints weight = 6887.061| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.03 r_work: 0.3440 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8196 Z= 0.151 Angle : 0.524 5.527 11136 Z= 0.273 Chirality : 0.039 0.132 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.507 12.369 1148 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.94 % Allowed : 14.27 % Favored : 84.79 % 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: 1.76 (0.26), residues: 1028 helix: 1.47 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.04 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.024 0.001 TYR A 273 PHE 0.015 0.001 PHE B 257 TRP 0.007 0.001 TRP D 172 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8196) covalent geometry : angle 0.52441 (11136) hydrogen bonds : bond 0.04551 ( 601) hydrogen bonds : angle 3.96102 ( 1767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.319 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 122 average time/residue: 0.0773 time to fit residues: 13.7017 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.0020 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.216884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169084 restraints weight = 6924.321| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.77 r_work: 0.3467 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8196 Z= 0.121 Angle : 0.496 5.155 11136 Z= 0.258 Chirality : 0.037 0.133 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.418 12.183 1148 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.71 % Allowed : 14.86 % Favored : 84.43 % 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: 2.47 (0.26), residues: 1028 helix: 2.02 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.44 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 256 TYR 0.023 0.001 TYR A 273 PHE 0.017 0.001 PHE B 257 TRP 0.006 0.001 TRP D 172 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8196) covalent geometry : angle 0.49634 (11136) hydrogen bonds : bond 0.04172 ( 601) hydrogen bonds : angle 3.80719 ( 1767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.225 Fit side-chains REVERT: C 301 PHE cc_start: 0.7820 (m-80) cc_final: 0.7404 (m-10) REVERT: D 301 PHE cc_start: 0.7842 (m-80) cc_final: 0.7428 (m-10) outliers start: 6 outliers final: 6 residues processed: 128 average time/residue: 0.0739 time to fit residues: 13.3934 Evaluate side-chains 127 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.215689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153994 restraints weight = 6944.012| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.84 r_work: 0.3366 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8196 Z= 0.139 Angle : 0.512 5.654 11136 Z= 0.267 Chirality : 0.038 0.133 1316 Planarity : 0.004 0.043 1364 Dihedral : 3.392 12.049 1148 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.83 % Allowed : 14.98 % Favored : 84.20 % 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: 2.45 (0.26), residues: 1028 helix: 2.00 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.45 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 256 TYR 0.021 0.001 TYR A 273 PHE 0.017 0.001 PHE B 257 TRP 0.006 0.001 TRP A 172 HIS 0.001 0.000 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8196) covalent geometry : angle 0.51165 (11136) hydrogen bonds : bond 0.04336 ( 601) hydrogen bonds : angle 3.82095 ( 1767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.259 Fit side-chains REVERT: A 346 GLU cc_start: 0.7658 (tt0) cc_final: 0.7409 (tt0) REVERT: B 301 PHE cc_start: 0.7820 (m-80) cc_final: 0.7389 (m-10) REVERT: C 301 PHE cc_start: 0.7729 (m-80) cc_final: 0.7304 (m-10) REVERT: D 301 PHE cc_start: 0.7806 (m-80) cc_final: 0.7352 (m-10) outliers start: 7 outliers final: 6 residues processed: 126 average time/residue: 0.0760 time to fit residues: 13.8399 Evaluate side-chains 127 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.215431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153433 restraints weight = 6871.555| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.94 r_work: 0.3351 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8196 Z= 0.143 Angle : 0.516 5.183 11136 Z= 0.269 Chirality : 0.039 0.131 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.393 12.088 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.71 % Allowed : 14.74 % Favored : 84.55 % 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: 2.45 (0.26), residues: 1028 helix: 2.00 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.46 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 256 TYR 0.020 0.001 TYR A 273 PHE 0.017 0.001 PHE C 257 TRP 0.006 0.001 TRP B 362 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8196) covalent geometry : angle 0.51616 (11136) hydrogen bonds : bond 0.04392 ( 601) hydrogen bonds : angle 3.83638 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.51 seconds wall clock time: 42 minutes 40.08 seconds (2560.08 seconds total)