Starting phenix.real_space_refine on Sun May 3 12:56:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ms_75844/05_2026/11ms_75844.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ms_75844/05_2026/11ms_75844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11ms_75844/05_2026/11ms_75844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ms_75844/05_2026/11ms_75844.map" model { file = "/net/cci-nas-00/data/ceres_data/11ms_75844/05_2026/11ms_75844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ms_75844/05_2026/11ms_75844.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7182 2.51 5 N 2067 2.21 5 O 3733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13036 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 486 Classifications: {'water': 486} Link IDs: {None: 485} Chain: "B" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 489 Classifications: {'water': 489} Link IDs: {None: 488} Chain: "C" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 508 Classifications: {'water': 508} Link IDs: {None: 507} Time building chain proxies: 3.42, per 1000 atoms: 0.26 Number of scatterers: 13036 At special positions: 0 Unit cell: (89.67, 85.995, 150.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 3733 8.00 N 2067 7.00 C 7182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 482 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 293 " distance=2.07 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 321 " distance=2.00 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 293 " distance=2.06 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 321 " distance=2.01 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 482 " distance=2.04 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 293 " distance=2.07 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 297 " - pdb=" SG CYS C 321 " distance=2.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 326.4 milliseconds 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 26.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.702A pdb=" N ASP A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 96 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.537A pdb=" N THR A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 472 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.759A pdb=" N ASP B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLY B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 96 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 383 through 401 Processing helix chain 'B' and resid 420 through 472 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.643A pdb=" N ASP C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY C 94 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 383 through 401 Processing helix chain 'C' and resid 420 through 472 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.238A pdb=" N ILE A 67 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 74 through 76 removed outlier: 6.804A pdb=" N LEU A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 103 " --> pdb=" O MET A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.570A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A 195 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE A 195 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.570A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A 195 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'A' and resid 152 through 156 removed outlier: 4.738A pdb=" N CYS A 155 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AB3, first strand: chain 'A' and resid 302 through 304 removed outlier: 4.403A pdb=" N CYS A 297 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 377 through 382 removed outlier: 4.687A pdb=" N TYR B 367 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB6, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AB7, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AB8, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.164A pdb=" N ILE B 67 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 74 through 76 removed outlier: 6.840A pdb=" N LEU B 75 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 103 " --> pdb=" O MET B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 138 removed outlier: 6.566A pdb=" N GLY B 272 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE B 195 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE B 195 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 138 removed outlier: 6.566A pdb=" N GLY B 272 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE B 195 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 156 removed outlier: 4.649A pdb=" N CYS B 155 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 180 through 185 Processing sheet with id=AC6, first strand: chain 'B' and resid 302 through 304 removed outlier: 4.167A pdb=" N CYS B 297 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 377 through 382 removed outlier: 4.799A pdb=" N TYR C 367 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AD2, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.213A pdb=" N ILE C 67 " --> pdb=" O GLY C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 74 through 76 removed outlier: 6.822A pdb=" N LEU C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE C 103 " --> pdb=" O MET C 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 116 through 117 removed outlier: 5.026A pdb=" N ILE C 195 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY C 272 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 117 removed outlier: 7.663A pdb=" N ILE C 195 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AD7, first strand: chain 'C' and resid 152 through 156 Processing sheet with id=AD8, first strand: chain 'C' and resid 180 through 185 Processing sheet with id=AD9, first strand: chain 'C' and resid 302 through 304 removed outlier: 4.134A pdb=" N CYS C 297 " --> pdb=" O ILE C 304 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1996 1.31 - 1.44: 3105 1.44 - 1.56: 6605 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 11778 Sorted by residual: bond pdb=" C PRO A 289 " pdb=" O PRO A 289 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.21e-02 6.83e+03 1.95e+01 bond pdb=" C PRO C 289 " pdb=" O PRO C 289 " ideal model delta sigma weight residual 1.233 1.183 0.050 1.19e-02 7.06e+03 1.75e+01 bond pdb=" CA SER A 295 " pdb=" CB SER A 295 " ideal model delta sigma weight residual 1.533 1.465 0.068 1.72e-02 3.38e+03 1.57e+01 bond pdb=" C PRO B 289 " pdb=" O PRO B 289 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.21e-02 6.83e+03 1.32e+01 bond pdb=" C PRO A 119 " pdb=" O PRO A 119 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.30e-02 5.92e+03 1.29e+01 ... (remaining 11773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 14895 1.61 - 3.22: 848 3.22 - 4.83: 155 4.83 - 6.44: 20 6.44 - 8.05: 12 Bond angle restraints: 15930 Sorted by residual: angle pdb=" CA TYR A 121 " pdb=" C TYR A 121 " pdb=" O TYR A 121 " ideal model delta sigma weight residual 120.82 116.28 4.54 1.05e+00 9.07e-01 1.87e+01 angle pdb=" N ASN A 405 " pdb=" CA ASN A 405 " pdb=" C ASN A 405 " ideal model delta sigma weight residual 110.50 104.73 5.77 1.41e+00 5.03e-01 1.68e+01 angle pdb=" C PRO B 119 " pdb=" CA PRO B 119 " pdb=" CB PRO B 119 " ideal model delta sigma weight residual 111.56 118.31 -6.75 1.65e+00 3.67e-01 1.67e+01 angle pdb=" CA ASP C 117 " pdb=" CB ASP C 117 " pdb=" CG ASP C 117 " ideal model delta sigma weight residual 112.60 116.65 -4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" C PRO A 119 " pdb=" CA PRO A 119 " pdb=" CB PRO A 119 " ideal model delta sigma weight residual 111.56 118.23 -6.67 1.65e+00 3.67e-01 1.64e+01 ... (remaining 15925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6507 17.96 - 35.92: 507 35.92 - 53.88: 98 53.88 - 71.83: 26 71.83 - 89.79: 20 Dihedral angle restraints: 7158 sinusoidal: 2934 harmonic: 4224 Sorted by residual: dihedral pdb=" C PRO B 119 " pdb=" N PRO B 119 " pdb=" CA PRO B 119 " pdb=" CB PRO B 119 " ideal model delta harmonic sigma weight residual -120.70 -132.87 12.17 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" N PRO B 119 " pdb=" C PRO B 119 " pdb=" CA PRO B 119 " pdb=" CB PRO B 119 " ideal model delta harmonic sigma weight residual 115.10 125.38 -10.28 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" CA CYS C 80 " pdb=" C CYS C 80 " pdb=" N THR C 81 " pdb=" CA THR C 81 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1636 0.115 - 0.230: 85 0.230 - 0.345: 4 0.345 - 0.459: 2 0.459 - 0.574: 1 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA PRO B 119 " pdb=" N PRO B 119 " pdb=" C PRO B 119 " pdb=" CB PRO B 119 " both_signs ideal model delta sigma weight residual False 2.72 2.14 0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" CA PRO C 119 " pdb=" N PRO C 119 " pdb=" C PRO C 119 " pdb=" CB PRO C 119 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA PRO A 119 " pdb=" N PRO A 119 " pdb=" C PRO A 119 " pdb=" CB PRO A 119 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1725 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 30 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C CYS C 30 " -0.037 2.00e-02 2.50e+03 pdb=" O CYS C 30 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 31 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 420 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C GLY B 420 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY B 420 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 421 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 295 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER A 295 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 295 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 296 " 0.012 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3631 2.81 - 3.33: 12039 3.33 - 3.85: 24966 3.85 - 4.38: 30571 4.38 - 4.90: 46978 Nonbonded interactions: 118185 Sorted by model distance: nonbonded pdb=" OE1 GLU C 57 " pdb=" OG1 THR C 329 " model vdw 2.286 3.040 nonbonded pdb=" O TRP C 143 " pdb=" O HOH C 601 " model vdw 2.301 3.040 nonbonded pdb=" O HOH C 675 " pdb=" O HOH C1093 " model vdw 2.308 3.040 nonbonded pdb=" OE2 GLU B 296 " pdb=" O HOH B 601 " model vdw 2.308 3.040 nonbonded pdb=" O ILE B 74 " pdb=" O HOH B 602 " model vdw 2.309 3.040 ... (remaining 118180 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 9.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11793 Z= 0.377 Angle : 0.840 8.045 15960 Z= 0.544 Chirality : 0.058 0.574 1728 Planarity : 0.004 0.030 2106 Dihedral : 14.341 89.792 4395 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.23 % Allowed : 1.56 % Favored : 98.20 % Cbeta Deviations : 0.07 % 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: 0.46 (0.20), residues: 1455 helix: 2.43 (0.26), residues: 351 sheet: 0.15 (0.26), residues: 351 loop : -0.63 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 472 TYR 0.012 0.002 TYR C 116 PHE 0.011 0.002 PHE C 408 TRP 0.010 0.002 TRP C 359 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00535 (11778) covalent geometry : angle 0.83569 (15930) SS BOND : bond 0.02161 ( 15) SS BOND : angle 2.16038 ( 30) hydrogen bonds : bond 0.09825 ( 489) hydrogen bonds : angle 6.30579 ( 1407) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7776 (mm110) cc_final: 0.7090 (pt0) REVERT: A 205 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7808 (ttpp) REVERT: A 296 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 461 ASN cc_start: 0.8070 (m-40) cc_final: 0.7741 (m-40) REVERT: A 462 LYS cc_start: 0.7940 (mtmt) cc_final: 0.7683 (mtmt) REVERT: A 469 LYS cc_start: 0.7690 (mttm) cc_final: 0.7406 (mptt) REVERT: B 31 LEU cc_start: 0.8818 (mp) cc_final: 0.8573 (mt) REVERT: B 43 LYS cc_start: 0.8619 (mttm) cc_final: 0.8333 (mttm) REVERT: B 47 ASN cc_start: 0.6891 (t0) cc_final: 0.6513 (t0) REVERT: B 49 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7495 (mtp-110) REVERT: B 91 GLN cc_start: 0.8018 (mm110) cc_final: 0.7323 (pt0) REVERT: B 224 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.6985 (mtm180) REVERT: B 384 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7102 (mptp) REVERT: B 417 GLU cc_start: 0.6912 (mm-30) cc_final: 0.5989 (pm20) REVERT: B 465 GLU cc_start: 0.8064 (tp30) cc_final: 0.7728 (tp30) REVERT: B 514 ASN cc_start: 0.8592 (m-40) cc_final: 0.8190 (m-40) REVERT: C 91 GLN cc_start: 0.7490 (mm110) cc_final: 0.7093 (pt0) REVERT: C 277 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7641 (mtm180) REVERT: C 280 LYS cc_start: 0.8155 (mttt) cc_final: 0.7681 (pttt) REVERT: C 448 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8233 (mm-30) REVERT: C 484 LYS cc_start: 0.8084 (tptm) cc_final: 0.7733 (tttm) outliers start: 3 outliers final: 0 residues processed: 213 average time/residue: 0.7674 time to fit residues: 175.1222 Evaluate side-chains 139 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 34 HIS A 262 ASN A 491 ASN A 514 ASN B 206 ASN B 226 GLN B 262 ASN B 405 ASN B 450 GLN B 513 ASN C 206 ASN C 262 ASN C 423 GLN C 470 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105326 restraints weight = 12000.803| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.51 r_work: 0.3076 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11793 Z= 0.115 Angle : 0.527 7.439 15960 Z= 0.279 Chirality : 0.044 0.146 1728 Planarity : 0.004 0.033 2106 Dihedral : 4.288 19.916 1584 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.48 % Allowed : 7.73 % Favored : 90.79 % 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: 0.76 (0.21), residues: 1455 helix: 2.94 (0.25), residues: 357 sheet: 0.38 (0.26), residues: 348 loop : -0.66 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.010 0.001 TYR B 507 PHE 0.011 0.001 PHE C 464 TRP 0.007 0.001 TRP A 437 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00259 (11778) covalent geometry : angle 0.52617 (15930) SS BOND : bond 0.00288 ( 15) SS BOND : angle 0.93879 ( 30) hydrogen bonds : bond 0.04728 ( 489) hydrogen bonds : angle 5.09226 ( 1407) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7777 (mm110) cc_final: 0.7128 (pt0) REVERT: A 205 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7987 (tttt) REVERT: A 296 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 417 GLU cc_start: 0.7082 (mp0) cc_final: 0.6676 (pm20) REVERT: A 426 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: A 461 ASN cc_start: 0.8299 (m-40) cc_final: 0.7981 (m-40) REVERT: A 462 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7748 (mtmt) REVERT: B 43 LYS cc_start: 0.8486 (mttm) cc_final: 0.8186 (mttm) REVERT: B 49 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7571 (mtp-110) REVERT: B 91 GLN cc_start: 0.8005 (mm110) cc_final: 0.7129 (pt0) REVERT: B 224 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.6921 (mtm180) REVERT: B 417 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6166 (pm20) REVERT: B 465 GLU cc_start: 0.8099 (tp30) cc_final: 0.7775 (tp30) REVERT: B 507 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: C 91 GLN cc_start: 0.7439 (mm110) cc_final: 0.6899 (pt0) REVERT: C 224 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7020 (mmt90) REVERT: C 277 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7620 (mtm180) REVERT: C 280 LYS cc_start: 0.8413 (mttt) cc_final: 0.7550 (pttt) REVERT: C 417 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: C 448 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8374 (mm-30) REVERT: C 484 LYS cc_start: 0.8062 (tptm) cc_final: 0.7763 (tttm) outliers start: 19 outliers final: 7 residues processed: 148 average time/residue: 0.7508 time to fit residues: 119.6501 Evaluate side-chains 142 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 470 GLN A 514 ASN B 138 ASN B 514 ASN C 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097829 restraints weight = 12155.730| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.54 r_work: 0.2977 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11793 Z= 0.304 Angle : 0.707 10.209 15960 Z= 0.376 Chirality : 0.054 0.191 1728 Planarity : 0.006 0.057 2106 Dihedral : 4.950 22.014 1584 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.64 % Allowed : 8.74 % Favored : 89.62 % 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: 0.51 (0.20), residues: 1455 helix: 2.67 (0.24), residues: 348 sheet: 0.20 (0.27), residues: 336 loop : -0.70 (0.19), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 108 TYR 0.016 0.003 TYR A 249 PHE 0.019 0.003 PHE A 369 TRP 0.011 0.002 TRP C 366 HIS 0.006 0.002 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00724 (11778) covalent geometry : angle 0.70583 (15930) SS BOND : bond 0.00464 ( 15) SS BOND : angle 1.08440 ( 30) hydrogen bonds : bond 0.06503 ( 489) hydrogen bonds : angle 5.50800 ( 1407) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7803 (mm110) cc_final: 0.7043 (pt0) REVERT: A 205 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7932 (tttm) REVERT: A 399 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6715 (mmm160) REVERT: A 451 HIS cc_start: 0.8422 (m90) cc_final: 0.8116 (m-70) REVERT: B 43 LYS cc_start: 0.8592 (mttm) cc_final: 0.8252 (mttm) REVERT: B 49 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7316 (mtp-110) REVERT: B 91 GLN cc_start: 0.8044 (mm110) cc_final: 0.6950 (pt0) REVERT: B 224 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.6949 (mtm180) REVERT: B 277 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7633 (mtm180) REVERT: B 384 LYS cc_start: 0.7841 (ttmt) cc_final: 0.6985 (mptp) REVERT: B 465 GLU cc_start: 0.8157 (tp30) cc_final: 0.7843 (tp30) REVERT: C 49 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7617 (ttm-80) REVERT: C 91 GLN cc_start: 0.7543 (mm110) cc_final: 0.6850 (pt0) REVERT: C 205 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8285 (tttm) REVERT: C 224 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7114 (mmt90) REVERT: C 258 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8469 (pt) REVERT: C 277 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7615 (mtm180) REVERT: C 280 LYS cc_start: 0.8371 (mttt) cc_final: 0.7496 (pttt) REVERT: C 294 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: C 384 LYS cc_start: 0.7158 (mtpt) cc_final: 0.6343 (mppt) REVERT: C 417 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: C 484 LYS cc_start: 0.8058 (tptm) cc_final: 0.7758 (tttm) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 0.7363 time to fit residues: 114.2684 Evaluate side-chains 144 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 470 GLN A 491 ASN A 514 ASN B 226 GLN B 514 ASN C 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103058 restraints weight = 12090.620| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.53 r_work: 0.3045 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11793 Z= 0.118 Angle : 0.511 7.012 15960 Z= 0.272 Chirality : 0.044 0.147 1728 Planarity : 0.004 0.052 2106 Dihedral : 4.354 19.364 1584 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.03 % Allowed : 8.35 % Favored : 89.62 % 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: 0.82 (0.20), residues: 1455 helix: 3.09 (0.25), residues: 354 sheet: 0.25 (0.26), residues: 348 loop : -0.57 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.010 0.001 TYR B 507 PHE 0.011 0.001 PHE A 369 TRP 0.008 0.001 TRP A 437 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00264 (11778) covalent geometry : angle 0.51065 (15930) SS BOND : bond 0.00256 ( 15) SS BOND : angle 0.76203 ( 30) hydrogen bonds : bond 0.04851 ( 489) hydrogen bonds : angle 4.99989 ( 1407) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7799 (mm110) cc_final: 0.7080 (pt0) REVERT: A 205 LYS cc_start: 0.8386 (ttpp) cc_final: 0.8069 (tttt) REVERT: A 254 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8128 (mmmt) REVERT: A 372 GLN cc_start: 0.7970 (tt0) cc_final: 0.7398 (tm-30) REVERT: A 462 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7680 (mtmt) REVERT: B 43 LYS cc_start: 0.8588 (mttm) cc_final: 0.8279 (mttm) REVERT: B 49 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7262 (mtp-110) REVERT: B 91 GLN cc_start: 0.8030 (mm110) cc_final: 0.6906 (pt0) REVERT: B 224 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.6930 (mtm180) REVERT: B 277 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7516 (mtp180) REVERT: B 384 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7123 (mptp) REVERT: B 417 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6308 (pm20) REVERT: B 465 GLU cc_start: 0.8147 (tp30) cc_final: 0.7829 (tp30) REVERT: C 49 ARG cc_start: 0.7825 (mtt180) cc_final: 0.6817 (ttt90) REVERT: C 91 GLN cc_start: 0.7608 (mm110) cc_final: 0.6912 (pt0) REVERT: C 224 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7096 (mmt90) REVERT: C 258 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8446 (pt) REVERT: C 277 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7691 (mtm180) REVERT: C 280 LYS cc_start: 0.8375 (mttt) cc_final: 0.7505 (pttt) REVERT: C 336 MET cc_start: 0.9113 (ptm) cc_final: 0.8904 (ptp) REVERT: C 417 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7117 (pt0) REVERT: C 448 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8387 (mm-30) REVERT: C 484 LYS cc_start: 0.8073 (tptm) cc_final: 0.7760 (tttm) outliers start: 26 outliers final: 8 residues processed: 151 average time/residue: 0.7189 time to fit residues: 117.2033 Evaluate side-chains 141 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.0870 chunk 118 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 213 GLN A 514 ASN B 226 GLN B 514 ASN C 206 ASN C 262 ASN C 514 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.100086 restraints weight = 12076.455| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.56 r_work: 0.3006 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11793 Z= 0.162 Angle : 0.553 8.765 15960 Z= 0.293 Chirality : 0.046 0.147 1728 Planarity : 0.004 0.054 2106 Dihedral : 4.484 20.461 1584 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.42 % Allowed : 9.06 % Favored : 88.52 % 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: 0.75 (0.20), residues: 1455 helix: 3.12 (0.24), residues: 351 sheet: 0.16 (0.25), residues: 369 loop : -0.64 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.009 0.002 TYR A 502 PHE 0.014 0.002 PHE A 369 TRP 0.007 0.001 TRP A 437 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00377 (11778) covalent geometry : angle 0.55256 (15930) SS BOND : bond 0.00257 ( 15) SS BOND : angle 0.75956 ( 30) hydrogen bonds : bond 0.05294 ( 489) hydrogen bonds : angle 5.10826 ( 1407) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7845 (mm110) cc_final: 0.7036 (pt0) REVERT: A 205 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8047 (tttt) REVERT: A 254 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8166 (mmmt) REVERT: A 372 GLN cc_start: 0.7935 (tt0) cc_final: 0.7352 (tm-30) REVERT: A 399 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6781 (mmm160) REVERT: A 462 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7682 (mtmt) REVERT: B 43 LYS cc_start: 0.8581 (mttm) cc_final: 0.8268 (mttm) REVERT: B 49 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7336 (mtp-110) REVERT: B 224 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.6929 (mtm180) REVERT: B 277 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7546 (mtm180) REVERT: B 384 LYS cc_start: 0.7786 (ttmt) cc_final: 0.6957 (mptp) REVERT: B 417 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6694 (pt0) REVERT: B 465 GLU cc_start: 0.8139 (tp30) cc_final: 0.7815 (tp30) REVERT: B 500 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6625 (mm-30) REVERT: C 49 ARG cc_start: 0.7783 (mtt180) cc_final: 0.6779 (ttt90) REVERT: C 91 GLN cc_start: 0.7602 (mm110) cc_final: 0.6873 (pt0) REVERT: C 224 ARG cc_start: 0.7573 (ttp80) cc_final: 0.7057 (mmt90) REVERT: C 258 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8470 (pt) REVERT: C 277 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7698 (mtm180) REVERT: C 280 LYS cc_start: 0.8326 (mttt) cc_final: 0.7436 (pttt) REVERT: C 294 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7995 (tttm) REVERT: C 336 MET cc_start: 0.9101 (ptm) cc_final: 0.8884 (ptp) REVERT: C 384 LYS cc_start: 0.7105 (mtpt) cc_final: 0.6329 (mppt) REVERT: C 417 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: C 448 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8300 (mm-30) REVERT: C 484 LYS cc_start: 0.8049 (tptm) cc_final: 0.7713 (tttm) outliers start: 31 outliers final: 14 residues processed: 159 average time/residue: 0.7015 time to fit residues: 120.6027 Evaluate side-chains 154 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 491 ASN A 514 ASN B 226 GLN B 514 ASN C 206 ASN C 262 ASN C 514 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102655 restraints weight = 11971.559| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.52 r_work: 0.3038 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11793 Z= 0.125 Angle : 0.510 7.789 15960 Z= 0.270 Chirality : 0.044 0.145 1728 Planarity : 0.004 0.051 2106 Dihedral : 4.294 19.484 1584 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.03 % Allowed : 9.68 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1455 helix: 3.23 (0.25), residues: 354 sheet: 0.22 (0.26), residues: 354 loop : -0.59 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.009 0.001 TYR A 502 PHE 0.011 0.001 PHE A 369 TRP 0.008 0.001 TRP A 437 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00282 (11778) covalent geometry : angle 0.50996 (15930) SS BOND : bond 0.00226 ( 15) SS BOND : angle 0.69866 ( 30) hydrogen bonds : bond 0.04863 ( 489) hydrogen bonds : angle 4.95738 ( 1407) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7826 (mm110) cc_final: 0.7029 (pt0) REVERT: A 205 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8050 (tttt) REVERT: A 372 GLN cc_start: 0.7981 (tt0) cc_final: 0.7440 (tm-30) REVERT: A 461 ASN cc_start: 0.8343 (m-40) cc_final: 0.8131 (m-40) REVERT: A 462 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7725 (mtmt) REVERT: B 43 LYS cc_start: 0.8583 (mttm) cc_final: 0.8274 (mttm) REVERT: B 49 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7246 (mtp-110) REVERT: B 224 ARG cc_start: 0.7806 (mtp-110) cc_final: 0.6935 (mtm180) REVERT: B 277 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7567 (mtm180) REVERT: B 384 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7081 (mptp) REVERT: B 417 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6769 (pt0) REVERT: B 465 GLU cc_start: 0.8147 (tp30) cc_final: 0.7834 (tp30) REVERT: B 500 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: C 49 ARG cc_start: 0.7834 (mtt180) cc_final: 0.6866 (ttt90) REVERT: C 91 GLN cc_start: 0.7627 (mm110) cc_final: 0.6938 (pt0) REVERT: C 224 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7101 (mmt90) REVERT: C 258 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8476 (pt) REVERT: C 277 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.7857 (mtm180) REVERT: C 280 LYS cc_start: 0.8353 (mttt) cc_final: 0.7487 (pttt) REVERT: C 417 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: C 448 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8394 (mm-30) REVERT: C 484 LYS cc_start: 0.8124 (tptm) cc_final: 0.7818 (tttm) outliers start: 26 outliers final: 14 residues processed: 153 average time/residue: 0.7223 time to fit residues: 119.4017 Evaluate side-chains 147 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 0.0010 chunk 141 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 514 ASN B 226 GLN B 514 ASN C 206 ASN C 262 ASN C 514 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104119 restraints weight = 12009.854| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.51 r_work: 0.3061 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11793 Z= 0.102 Angle : 0.481 7.483 15960 Z= 0.254 Chirality : 0.043 0.144 1728 Planarity : 0.004 0.049 2106 Dihedral : 4.098 18.523 1584 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.80 % Allowed : 10.07 % Favored : 88.13 % 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: 1.05 (0.21), residues: 1455 helix: 3.43 (0.25), residues: 354 sheet: 0.38 (0.26), residues: 345 loop : -0.49 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.009 0.001 TYR B 507 PHE 0.010 0.001 PHE A 369 TRP 0.008 0.001 TRP A 437 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00223 (11778) covalent geometry : angle 0.48094 (15930) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.64439 ( 30) hydrogen bonds : bond 0.04472 ( 489) hydrogen bonds : angle 4.78654 ( 1407) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7803 (mm110) cc_final: 0.6996 (pt0) REVERT: A 205 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8020 (tttt) REVERT: A 372 GLN cc_start: 0.7897 (tt0) cc_final: 0.7375 (tm-30) REVERT: A 426 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8564 (mt-10) REVERT: A 462 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7685 (mtmt) REVERT: B 43 LYS cc_start: 0.8556 (mttm) cc_final: 0.8245 (mttm) REVERT: B 49 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.7219 (mtp-110) REVERT: B 224 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.6890 (mtm180) REVERT: B 277 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7531 (mtm180) REVERT: B 384 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7050 (mptp) REVERT: B 417 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6488 (pm20) REVERT: B 465 GLU cc_start: 0.8127 (tp30) cc_final: 0.7817 (tp30) REVERT: C 49 ARG cc_start: 0.7779 (mtt180) cc_final: 0.6847 (ttt90) REVERT: C 91 GLN cc_start: 0.7588 (mm110) cc_final: 0.6885 (pt0) REVERT: C 258 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8458 (pt) REVERT: C 277 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7835 (mtm180) REVERT: C 280 LYS cc_start: 0.8336 (mttt) cc_final: 0.7469 (pttt) REVERT: C 417 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: C 448 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8414 (mm-30) REVERT: C 484 LYS cc_start: 0.8080 (tptm) cc_final: 0.7755 (tttm) REVERT: C 491 ASN cc_start: 0.7587 (m-40) cc_final: 0.7324 (m-40) outliers start: 23 outliers final: 14 residues processed: 151 average time/residue: 0.6294 time to fit residues: 102.8811 Evaluate side-chains 146 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 73 optimal weight: 0.0870 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 514 ASN B 226 GLN B 514 ASN C 206 ASN C 232 ASN C 262 ASN C 514 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102964 restraints weight = 11857.056| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.51 r_work: 0.3045 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11793 Z= 0.122 Angle : 0.506 8.574 15960 Z= 0.267 Chirality : 0.044 0.144 1728 Planarity : 0.004 0.049 2106 Dihedral : 4.215 19.415 1584 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.03 % Allowed : 10.23 % Favored : 87.74 % 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: 1.00 (0.21), residues: 1455 helix: 3.36 (0.25), residues: 354 sheet: 0.29 (0.26), residues: 348 loop : -0.48 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.008 0.001 TYR A 502 PHE 0.012 0.001 PHE A 369 TRP 0.008 0.001 TRP C 250 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00274 (11778) covalent geometry : angle 0.50596 (15930) SS BOND : bond 0.00221 ( 15) SS BOND : angle 0.67303 ( 30) hydrogen bonds : bond 0.04774 ( 489) hydrogen bonds : angle 4.88666 ( 1407) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7778 (mm110) cc_final: 0.6971 (pt0) REVERT: A 205 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8043 (tttt) REVERT: A 372 GLN cc_start: 0.7907 (tt0) cc_final: 0.7369 (tm-30) REVERT: A 426 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8606 (mt-10) REVERT: A 462 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7776 (mtmt) REVERT: B 43 LYS cc_start: 0.8574 (mttm) cc_final: 0.8272 (mttm) REVERT: B 49 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7238 (mtp-110) REVERT: B 224 ARG cc_start: 0.7810 (mtp-110) cc_final: 0.6930 (mtm180) REVERT: B 277 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7538 (mtm180) REVERT: B 384 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7039 (mptp) REVERT: B 417 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6524 (pm20) REVERT: B 465 GLU cc_start: 0.8149 (tp30) cc_final: 0.7854 (tp30) REVERT: B 500 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6671 (mm-30) REVERT: C 50 ILE cc_start: 0.8201 (mt) cc_final: 0.7998 (mm) REVERT: C 91 GLN cc_start: 0.7602 (mm110) cc_final: 0.6861 (pt0) REVERT: C 258 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8480 (pt) REVERT: C 277 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7848 (mtm180) REVERT: C 280 LYS cc_start: 0.8333 (mttt) cc_final: 0.7476 (pttt) REVERT: C 294 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7949 (tttm) REVERT: C 384 LYS cc_start: 0.7132 (mtpt) cc_final: 0.6360 (mppt) REVERT: C 417 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7125 (pt0) REVERT: C 448 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8392 (mm-30) REVERT: C 484 LYS cc_start: 0.8112 (tptm) cc_final: 0.7787 (tttm) REVERT: C 491 ASN cc_start: 0.7600 (m-40) cc_final: 0.7353 (m-40) outliers start: 26 outliers final: 16 residues processed: 147 average time/residue: 0.7057 time to fit residues: 112.0598 Evaluate side-chains 148 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 122 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 491 ASN A 514 ASN B 499 ASN B 514 ASN C 138 ASN C 206 ASN C 262 ASN C 514 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.097498 restraints weight = 12055.767| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.54 r_work: 0.2972 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11793 Z= 0.314 Angle : 0.695 10.802 15960 Z= 0.369 Chirality : 0.054 0.189 1728 Planarity : 0.005 0.055 2106 Dihedral : 4.903 21.697 1584 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.19 % Allowed : 10.46 % Favored : 87.35 % 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: 0.62 (0.20), residues: 1455 helix: 2.88 (0.24), residues: 354 sheet: 0.12 (0.26), residues: 354 loop : -0.66 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 224 TYR 0.016 0.003 TYR A 249 PHE 0.021 0.003 PHE A 369 TRP 0.010 0.002 TRP B 196 HIS 0.007 0.002 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00744 (11778) covalent geometry : angle 0.69402 (15930) SS BOND : bond 0.00454 ( 15) SS BOND : angle 1.06119 ( 30) hydrogen bonds : bond 0.06462 ( 489) hydrogen bonds : angle 5.39014 ( 1407) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7824 (mm110) cc_final: 0.6985 (pt0) REVERT: A 205 LYS cc_start: 0.8364 (ttpp) cc_final: 0.7981 (tttm) REVERT: B 43 LYS cc_start: 0.8585 (mttm) cc_final: 0.8371 (mttm) REVERT: B 49 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7393 (mtp-110) REVERT: B 224 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.6974 (mtm180) REVERT: B 277 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7665 (mtm180) REVERT: B 384 LYS cc_start: 0.7858 (ttmt) cc_final: 0.6974 (mptp) REVERT: B 417 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6972 (mm-30) REVERT: B 465 GLU cc_start: 0.8182 (tp30) cc_final: 0.7892 (tp30) REVERT: C 91 GLN cc_start: 0.7695 (mm110) cc_final: 0.6936 (pt0) REVERT: C 258 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8514 (pt) REVERT: C 277 ARG cc_start: 0.8391 (mtt-85) cc_final: 0.7851 (mtm180) REVERT: C 280 LYS cc_start: 0.8351 (mttt) cc_final: 0.7477 (pttt) REVERT: C 294 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8281 (tttm) REVERT: C 384 LYS cc_start: 0.7163 (mtpt) cc_final: 0.6350 (mppt) REVERT: C 417 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: C 448 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8298 (mm-30) REVERT: C 484 LYS cc_start: 0.8191 (tptm) cc_final: 0.7878 (tttm) REVERT: C 513 ASN cc_start: 0.7507 (m110) cc_final: 0.7244 (m-40) outliers start: 28 outliers final: 16 residues processed: 147 average time/residue: 0.6662 time to fit residues: 106.0056 Evaluate side-chains 145 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 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 34 HIS A 491 ASN A 513 ASN A 514 ASN B 226 GLN B 499 ASN B 514 ASN C 206 ASN C 262 ASN C 514 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101892 restraints weight = 12021.454| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.53 r_work: 0.3031 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11793 Z= 0.137 Angle : 0.526 8.359 15960 Z= 0.279 Chirality : 0.045 0.149 1728 Planarity : 0.004 0.052 2106 Dihedral : 4.425 19.842 1584 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.56 % Allowed : 11.16 % Favored : 87.28 % 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: 0.84 (0.20), residues: 1455 helix: 3.20 (0.25), residues: 354 sheet: 0.21 (0.26), residues: 348 loop : -0.58 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.009 0.001 TYR B 507 PHE 0.012 0.002 PHE A 369 TRP 0.007 0.001 TRP A 437 HIS 0.008 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00310 (11778) covalent geometry : angle 0.52559 (15930) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.70674 ( 30) hydrogen bonds : bond 0.05012 ( 489) hydrogen bonds : angle 4.99497 ( 1407) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.521 Fit side-chains REVERT: A 91 GLN cc_start: 0.7779 (mm110) cc_final: 0.6947 (pt0) REVERT: A 205 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8085 (tttt) REVERT: A 372 GLN cc_start: 0.7916 (tt0) cc_final: 0.7316 (tm-30) REVERT: A 451 HIS cc_start: 0.8408 (m90) cc_final: 0.8108 (m-70) REVERT: A 462 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7784 (mtmt) REVERT: B 43 LYS cc_start: 0.8586 (mttm) cc_final: 0.8264 (mttm) REVERT: B 49 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7288 (mtp-110) REVERT: B 224 ARG cc_start: 0.7822 (mtp-110) cc_final: 0.6962 (mtm180) REVERT: B 277 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7678 (mtm180) REVERT: B 384 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7036 (mptp) REVERT: B 417 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7031 (mm-30) REVERT: B 465 GLU cc_start: 0.8144 (tp30) cc_final: 0.7863 (tp30) REVERT: C 50 ILE cc_start: 0.8234 (mt) cc_final: 0.8029 (mm) REVERT: C 91 GLN cc_start: 0.7693 (mm110) cc_final: 0.6982 (pt0) REVERT: C 258 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8475 (pt) REVERT: C 277 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.7927 (mtm180) REVERT: C 280 LYS cc_start: 0.8357 (mttt) cc_final: 0.7496 (pttt) REVERT: C 294 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7967 (tttm) REVERT: C 384 LYS cc_start: 0.7110 (mtpt) cc_final: 0.6360 (mppt) REVERT: C 417 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7198 (pt0) REVERT: C 448 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 484 LYS cc_start: 0.8151 (tptm) cc_final: 0.7784 (tttm) REVERT: C 491 ASN cc_start: 0.7648 (m-40) cc_final: 0.7397 (m-40) REVERT: C 513 ASN cc_start: 0.7586 (m110) cc_final: 0.7363 (m-40) outliers start: 20 outliers final: 14 residues processed: 148 average time/residue: 0.7509 time to fit residues: 119.6112 Evaluate side-chains 148 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 513 ASN A 514 ASN B 226 GLN B 514 ASN C 206 ASN C 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.099008 restraints weight = 11950.916| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.54 r_work: 0.2993 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11793 Z= 0.203 Angle : 0.592 9.469 15960 Z= 0.314 Chirality : 0.048 0.155 1728 Planarity : 0.004 0.054 2106 Dihedral : 4.649 20.994 1584 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.72 % Allowed : 11.09 % Favored : 87.20 % 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: 0.78 (0.20), residues: 1455 helix: 3.09 (0.24), residues: 354 sheet: 0.18 (0.26), residues: 348 loop : -0.59 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 224 TYR 0.010 0.002 TYR C 439 PHE 0.016 0.002 PHE A 369 TRP 0.007 0.001 TRP B 437 HIS 0.008 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00476 (11778) covalent geometry : angle 0.59149 (15930) SS BOND : bond 0.00300 ( 15) SS BOND : angle 0.80268 ( 30) hydrogen bonds : bond 0.05628 ( 489) hydrogen bonds : angle 5.17129 ( 1407) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5116.34 seconds wall clock time: 88 minutes 3.46 seconds (5283.46 seconds total)