Starting phenix.real_space_refine on Fri Jul 3 15:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.map" model { file = "/net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sd3_40349/07_2026/8sd3_40349.cif" } resolution = 2.95 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= 0.006 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 8 5.49 5 S 36 5.16 5 C 5276 2.51 5 N 1156 2.21 5 O 1352 1.98 5 H 6824 0.53 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 122 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 2, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Unusual residues: {' K': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 2, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 2.83, per 1000 atoms: 0.19 Number of scatterers: 14656 At special positions: 0 Unit cell: (107.06, 107.06, 69.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 36 16.00 P 8 15.00 O 1352 8.00 N 1156 7.00 C 5276 6.00 H 6824 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 446.4 milliseconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 87.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.521A pdb=" N TYR A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 4.261A pdb=" N ILE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.838A pdb=" N ARG A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 306 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 350 Processing helix chain 'A' and resid 359 through 372 removed outlier: 4.146A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.759A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.948A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.521A pdb=" N TYR B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 removed outlier: 4.261A pdb=" N ILE B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.837A pdb=" N ARG B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 306 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 350 Processing helix chain 'B' and resid 359 through 372 removed outlier: 4.147A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 403 removed outlier: 3.759A pdb=" N ILE B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.949A pdb=" N ILE B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 266 through 277 removed outlier: 3.521A pdb=" N TYR C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 removed outlier: 4.262A pdb=" N ILE C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 removed outlier: 3.837A pdb=" N ARG C 302 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 306 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 350 Processing helix chain 'C' and resid 359 through 372 removed outlier: 4.146A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 403 removed outlier: 3.760A pdb=" N ILE C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 428 removed outlier: 3.949A pdb=" N ILE C 408 " --> pdb=" O PRO C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.520A pdb=" N TYR D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 298 removed outlier: 4.262A pdb=" N ILE D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 removed outlier: 3.838A pdb=" N ARG D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 306 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 350 Processing helix chain 'D' and resid 359 through 372 removed outlier: 4.146A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.759A pdb=" N ILE D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 428 removed outlier: 3.948A pdb=" N ILE D 408 " --> pdb=" O PRO D 404 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1632 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: 2.95 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6812 1.03 - 1.22: 52 1.22 - 1.42: 3044 1.42 - 1.61: 4820 1.61 - 1.81: 68 Bond restraints: 14796 Sorted by residual: bond pdb=" C21 POV B1004 " pdb=" O21 POV B1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV C1004 " pdb=" O21 POV C1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV D1004 " pdb=" O21 POV D1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C21 POV A1004 " pdb=" O21 POV A1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C21 POV A1003 " pdb=" O21 POV A1003 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 14791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 25755 2.07 - 4.14: 339 4.14 - 6.21: 126 6.21 - 8.28: 44 8.28 - 10.35: 36 Bond angle restraints: 26300 Sorted by residual: angle pdb=" C32 POV B1002 " pdb=" C31 POV B1002 " pdb=" O31 POV B1002 " ideal model delta sigma weight residual 110.66 121.01 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C32 POV A1002 " pdb=" C31 POV A1002 " pdb=" O31 POV A1002 " ideal model delta sigma weight residual 110.66 120.96 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV D1002 " pdb=" C31 POV D1002 " pdb=" O31 POV D1002 " ideal model delta sigma weight residual 110.66 120.96 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV C1002 " pdb=" C31 POV C1002 " pdb=" O31 POV C1002 " ideal model delta sigma weight residual 110.66 120.95 -10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV C1003 " pdb=" C31 POV C1003 " pdb=" O31 POV C1003 " ideal model delta sigma weight residual 110.66 120.68 -10.02 3.00e+00 1.11e-01 1.12e+01 ... (remaining 26295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 6672 21.11 - 42.22: 300 42.22 - 63.32: 144 63.32 - 84.43: 24 84.43 - 105.54: 12 Dihedral angle restraints: 7152 sinusoidal: 3844 harmonic: 3308 Sorted by residual: dihedral pdb=" C3 POV D1001 " pdb=" C31 POV D1001 " pdb=" O31 POV D1001 " pdb=" C32 POV D1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.85 -105.54 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C3 POV A1001 " pdb=" C31 POV A1001 " pdb=" O31 POV A1001 " pdb=" C32 POV A1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.87 -105.52 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C3 POV C1001 " pdb=" C31 POV C1001 " pdb=" O31 POV C1001 " pdb=" C32 POV C1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.89 -105.50 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 7149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1110 0.067 - 0.134: 147 0.134 - 0.201: 3 0.201 - 0.268: 0 0.268 - 0.335: 4 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CG LEU D 207 " pdb=" CB LEU D 207 " pdb=" CD1 LEU D 207 " pdb=" CD2 LEU D 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU A 207 " pdb=" CB LEU A 207 " pdb=" CD1 LEU A 207 " pdb=" CD2 LEU A 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU B 207 " pdb=" CB LEU B 207 " pdb=" CD1 LEU B 207 " pdb=" CD2 LEU B 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1261 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 254 " -0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE B 254 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 254 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 254 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE B 254 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 254 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 254 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 254 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE B 254 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE B 254 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE B 254 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE B 254 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 254 " -0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE A 254 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 254 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 254 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 254 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 254 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 254 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 254 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 254 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE A 254 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 254 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 254 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 254 " 0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE C 254 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE C 254 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 254 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE C 254 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 254 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 254 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE C 254 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE C 254 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE C 254 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE C 254 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 254 " 0.013 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.47: 8394 2.47 - 3.14: 39699 3.14 - 3.81: 49736 3.81 - 4.47: 74365 4.47 - 5.14: 112037 Nonbonded interactions: 284231 Sorted by model distance: nonbonded pdb=" HZ3 LYS D 356 " pdb=" O ASP D 378 " model vdw 1.808 2.450 nonbonded pdb=" HZ3 LYS A 356 " pdb=" O ASP A 378 " model vdw 1.808 2.450 nonbonded pdb=" HZ3 LYS B 356 " pdb=" O ASP B 378 " model vdw 1.808 2.450 nonbonded pdb=" HZ3 LYS C 356 " pdb=" O ASP C 378 " model vdw 1.808 2.450 nonbonded pdb=" O THR A 372 " pdb=" HG1 THR A 373 " model vdw 1.813 2.450 ... (remaining 284226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 171 through 428 or (resid 1001 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name O22)) or resid 1002 or (r \ esid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O21 or name O22 or name O31 or \ name O32)) or (resid 1004 and (name C1 or name C2 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name O21 or \ name O22)) or resid 1005 through 1006)) selection = (chain 'B' and (resid 171 through 1001 or (resid 1002 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name O21 or name O22 or name O31 or name O32)) or (resid 1003 and (name \ C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name O21 or name O22)) or (resid 1004 through 1 \ 005 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name O22)))) selection = (chain 'C' and (resid 171 through 428 or (resid 1001 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name O22)) or resid 1002 or (r \ esid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O21 or name O22 or name O31 or \ name O32)) or (resid 1004 and (name C1 or name C2 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name O21 or \ name O22)) or resid 1005 through 1006)) selection = (chain 'D' and (resid 171 through 1001 or (resid 1002 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name O21 or name O22 or name O31 or name O32)) or (resid 1003 and (name \ C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name O21 or name O22)) or (resid 1004 through 1 \ 005 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name O22)))) } 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: 0.920 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.150 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.010 0.128 7972 Z= 0.461 Angle : 1.079 10.351 10752 Z= 0.445 Chirality : 0.045 0.335 1264 Planarity : 0.005 0.047 1264 Dihedral : 15.421 105.541 2884 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 1.86 (0.28), residues: 924 helix: 1.53 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.27 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 302 TYR 0.009 0.002 TYR A 376 PHE 0.085 0.003 PHE B 254 TRP 0.008 0.001 TRP D 365 HIS 0.001 0.000 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00979 / 0.46 ( 7972) covalent geometry : angle 1.07935 / 0.45 (10752) hydrogen bonds : bond 0.11092 / 7.12 ( 564) hydrogen bonds : angle 4.96460 / 3.32 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.8761 time to fit residues: 105.6675 Evaluate side-chains 100 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 205 ASN B 179 ASN B 205 ASN C 179 ASN D 179 ASN D 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113554 restraints weight = 23321.419| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.00 r_work: 0.3111 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7972 Z= 0.114 Angle : 0.512 4.387 10752 Z= 0.260 Chirality : 0.036 0.113 1264 Planarity : 0.005 0.048 1264 Dihedral : 13.886 82.348 1260 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.68 % Allowed : 6.35 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.29), residues: 924 helix: 2.02 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.09 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 299 TYR 0.003 0.001 TYR B 416 PHE 0.015 0.001 PHE B 244 TRP 0.009 0.001 TRP C 365 HIS 0.001 0.000 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 7972) covalent geometry : angle 0.51233 / 0.26 (10752) hydrogen bonds : bond 0.03695 / 2.44 ( 564) hydrogen bonds : angle 4.16196 / 2.83 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.337 Fit side-chains REVERT: A 356 LYS cc_start: 0.8885 (mttt) cc_final: 0.8622 (mttm) REVERT: A 378 ASP cc_start: 0.9028 (p0) cc_final: 0.8812 (p0) REVERT: B 356 LYS cc_start: 0.8905 (mttt) cc_final: 0.8649 (mttm) REVERT: B 378 ASP cc_start: 0.9049 (p0) cc_final: 0.8823 (OUTLIER) REVERT: C 356 LYS cc_start: 0.8963 (mttt) cc_final: 0.8678 (mttm) REVERT: C 378 ASP cc_start: 0.9020 (p0) cc_final: 0.8658 (p0) REVERT: D 356 LYS cc_start: 0.8914 (mttt) cc_final: 0.8645 (mttm) REVERT: D 378 ASP cc_start: 0.9038 (p0) cc_final: 0.8719 (p0) outliers start: 13 outliers final: 5 residues processed: 134 average time/residue: 0.7850 time to fit residues: 113.8236 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.105623 restraints weight = 24252.002| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.99 r_work: 0.2990 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7972 Z= 0.171 Angle : 0.522 4.206 10752 Z= 0.269 Chirality : 0.037 0.124 1264 Planarity : 0.006 0.050 1264 Dihedral : 13.255 80.309 1260 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.04 % Allowed : 10.23 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.28), residues: 924 helix: 1.94 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.00 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.005 0.001 TYR C 270 PHE 0.016 0.001 PHE C 244 TRP 0.008 0.001 TRP A 365 HIS 0.002 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 7972) covalent geometry : angle 0.52228 / 0.27 (10752) hydrogen bonds : bond 0.04244 / 2.81 ( 564) hydrogen bonds : angle 4.15920 / 2.83 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.416 Fit side-chains REVERT: A 356 LYS cc_start: 0.9075 (mttt) cc_final: 0.8835 (mttm) REVERT: A 378 ASP cc_start: 0.9242 (p0) cc_final: 0.8951 (p0) REVERT: B 356 LYS cc_start: 0.9074 (mttt) cc_final: 0.8836 (mttm) REVERT: B 378 ASP cc_start: 0.9237 (p0) cc_final: 0.8940 (p0) REVERT: C 356 LYS cc_start: 0.9079 (mttt) cc_final: 0.8822 (mttm) REVERT: C 378 ASP cc_start: 0.9229 (p0) cc_final: 0.8913 (p0) REVERT: D 356 LYS cc_start: 0.9078 (mttt) cc_final: 0.8832 (mttm) REVERT: D 378 ASP cc_start: 0.9241 (p0) cc_final: 0.8937 (p0) outliers start: 8 outliers final: 9 residues processed: 132 average time/residue: 0.7665 time to fit residues: 109.6589 Evaluate side-chains 130 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 274 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106194 restraints weight = 23976.034| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.99 r_work: 0.3011 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7972 Z= 0.137 Angle : 0.478 4.158 10752 Z= 0.253 Chirality : 0.036 0.120 1264 Planarity : 0.005 0.050 1264 Dihedral : 12.513 77.369 1260 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.78 % Allowed : 9.97 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.28), residues: 924 helix: 2.00 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.23 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 296 TYR 0.004 0.001 TYR D 269 PHE 0.046 0.002 PHE C 274 TRP 0.007 0.001 TRP A 365 HIS 0.002 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7972) covalent geometry : angle 0.47811 / 0.25 (10752) hydrogen bonds : bond 0.03825 / 2.53 ( 564) hydrogen bonds : angle 4.03482 / 2.77 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.335 Fit side-chains REVERT: A 349 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8225 (mt-10) REVERT: A 356 LYS cc_start: 0.9078 (mttt) cc_final: 0.8820 (mttm) REVERT: A 378 ASP cc_start: 0.9189 (p0) cc_final: 0.8850 (p0) REVERT: B 356 LYS cc_start: 0.9078 (mttt) cc_final: 0.8827 (mttm) REVERT: B 378 ASP cc_start: 0.9209 (p0) cc_final: 0.8906 (p0) REVERT: C 356 LYS cc_start: 0.9070 (mttt) cc_final: 0.8810 (mttm) REVERT: C 378 ASP cc_start: 0.9189 (p0) cc_final: 0.8836 (p0) REVERT: D 356 LYS cc_start: 0.9093 (mttt) cc_final: 0.8839 (mttm) REVERT: D 378 ASP cc_start: 0.9219 (p0) cc_final: 0.8898 (p0) outliers start: 6 outliers final: 3 residues processed: 141 average time/residue: 0.7366 time to fit residues: 112.6234 Evaluate side-chains 125 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105895 restraints weight = 23966.573| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.94 r_work: 0.2986 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7972 Z= 0.137 Angle : 0.474 4.161 10752 Z= 0.247 Chirality : 0.035 0.119 1264 Planarity : 0.005 0.050 1264 Dihedral : 12.325 75.962 1260 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.78 % Allowed : 11.66 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.28), residues: 924 helix: 2.05 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.23 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 299 TYR 0.006 0.001 TYR C 270 PHE 0.022 0.001 PHE A 274 TRP 0.007 0.001 TRP D 365 HIS 0.002 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7972) covalent geometry : angle 0.47355 / 0.25 (10752) hydrogen bonds : bond 0.03776 / 2.51 ( 564) hydrogen bonds : angle 3.95147 / 2.70 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.393 Fit side-chains REVERT: A 349 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 356 LYS cc_start: 0.9081 (mttt) cc_final: 0.8818 (mttm) REVERT: A 378 ASP cc_start: 0.9184 (p0) cc_final: 0.8830 (p0) REVERT: B 356 LYS cc_start: 0.9087 (mttt) cc_final: 0.8833 (mttm) REVERT: B 378 ASP cc_start: 0.9207 (p0) cc_final: 0.8892 (p0) REVERT: C 356 LYS cc_start: 0.9093 (mttt) cc_final: 0.8812 (mttm) REVERT: C 378 ASP cc_start: 0.9180 (p0) cc_final: 0.8827 (p0) REVERT: D 356 LYS cc_start: 0.9049 (mttt) cc_final: 0.8782 (mttm) REVERT: D 378 ASP cc_start: 0.9215 (p0) cc_final: 0.8883 (p0) outliers start: 6 outliers final: 5 residues processed: 134 average time/residue: 0.8321 time to fit residues: 120.2394 Evaluate side-chains 133 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104628 restraints weight = 24368.407| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.97 r_work: 0.2985 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7972 Z= 0.168 Angle : 0.488 4.177 10752 Z= 0.256 Chirality : 0.036 0.125 1264 Planarity : 0.006 0.050 1264 Dihedral : 12.632 74.911 1260 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.78 % Allowed : 12.05 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.28), residues: 924 helix: 2.03 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.21 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 296 TYR 0.005 0.001 TYR A 270 PHE 0.016 0.001 PHE D 244 TRP 0.007 0.001 TRP D 365 HIS 0.002 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 7972) covalent geometry : angle 0.48806 / 0.26 (10752) hydrogen bonds : bond 0.04007 / 2.67 ( 564) hydrogen bonds : angle 3.97887 / 2.73 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.325 Fit side-chains REVERT: A 356 LYS cc_start: 0.9084 (mttt) cc_final: 0.8795 (mttm) REVERT: A 378 ASP cc_start: 0.9245 (p0) cc_final: 0.8907 (p0) REVERT: B 356 LYS cc_start: 0.9078 (mttt) cc_final: 0.8807 (mttm) REVERT: B 378 ASP cc_start: 0.9234 (p0) cc_final: 0.8917 (p0) REVERT: C 356 LYS cc_start: 0.9084 (mttt) cc_final: 0.8793 (mttm) REVERT: C 378 ASP cc_start: 0.9235 (p0) cc_final: 0.8906 (p0) REVERT: D 356 LYS cc_start: 0.9053 (mttt) cc_final: 0.8773 (mttm) REVERT: D 378 ASP cc_start: 0.9241 (p0) cc_final: 0.8910 (p0) outliers start: 6 outliers final: 5 residues processed: 141 average time/residue: 0.7487 time to fit residues: 114.6881 Evaluate side-chains 135 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104910 restraints weight = 24045.474| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.96 r_work: 0.2999 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7972 Z= 0.162 Angle : 0.492 5.243 10752 Z= 0.256 Chirality : 0.036 0.123 1264 Planarity : 0.006 0.050 1264 Dihedral : 12.791 74.218 1260 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.65 % Allowed : 12.69 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.28), residues: 924 helix: 2.05 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.18 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 296 TYR 0.005 0.001 TYR D 270 PHE 0.021 0.001 PHE B 244 TRP 0.007 0.001 TRP D 365 HIS 0.002 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 7972) covalent geometry : angle 0.49191 / 0.26 (10752) hydrogen bonds : bond 0.03977 / 2.65 ( 564) hydrogen bonds : angle 3.94765 / 2.71 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.435 Fit side-chains REVERT: A 324 TYR cc_start: 0.8528 (p90) cc_final: 0.8085 (p90) REVERT: A 356 LYS cc_start: 0.9079 (mttt) cc_final: 0.8790 (mttm) REVERT: A 378 ASP cc_start: 0.9261 (p0) cc_final: 0.8916 (p0) REVERT: B 356 LYS cc_start: 0.9087 (mttt) cc_final: 0.8796 (mttm) REVERT: B 378 ASP cc_start: 0.9238 (p0) cc_final: 0.8934 (p0) REVERT: C 356 LYS cc_start: 0.9081 (mttt) cc_final: 0.8786 (mttm) REVERT: C 378 ASP cc_start: 0.9243 (p0) cc_final: 0.8915 (p0) REVERT: D 356 LYS cc_start: 0.9078 (mttt) cc_final: 0.8784 (mttm) REVERT: D 378 ASP cc_start: 0.9246 (p0) cc_final: 0.8921 (p0) outliers start: 5 outliers final: 5 residues processed: 139 average time/residue: 0.8087 time to fit residues: 121.9360 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106094 restraints weight = 24153.367| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.01 r_work: 0.3033 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7972 Z= 0.119 Angle : 0.457 5.405 10752 Z= 0.237 Chirality : 0.035 0.117 1264 Planarity : 0.005 0.049 1264 Dihedral : 12.473 75.459 1260 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.78 % Allowed : 11.79 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.28), residues: 924 helix: 2.24 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.26 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 296 TYR 0.004 0.001 TYR A 270 PHE 0.018 0.001 PHE A 244 TRP 0.007 0.001 TRP C 365 HIS 0.002 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7972) covalent geometry : angle 0.45654 / 0.24 (10752) hydrogen bonds : bond 0.03560 / 2.36 ( 564) hydrogen bonds : angle 3.82897 / 2.63 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.380 Fit side-chains REVERT: A 356 LYS cc_start: 0.9089 (mttt) cc_final: 0.8803 (mttm) REVERT: A 378 ASP cc_start: 0.9239 (p0) cc_final: 0.8970 (p0) REVERT: B 356 LYS cc_start: 0.9091 (mttt) cc_final: 0.8801 (mttm) REVERT: B 378 ASP cc_start: 0.9219 (p0) cc_final: 0.8980 (p0) REVERT: C 356 LYS cc_start: 0.9094 (mttt) cc_final: 0.8803 (mttm) REVERT: C 378 ASP cc_start: 0.9220 (p0) cc_final: 0.8955 (p0) REVERT: D 356 LYS cc_start: 0.9072 (mttt) cc_final: 0.8797 (mttm) REVERT: D 378 ASP cc_start: 0.9234 (p0) cc_final: 0.8930 (p0) outliers start: 6 outliers final: 5 residues processed: 136 average time/residue: 0.7615 time to fit residues: 112.2522 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107064 restraints weight = 24083.754| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.95 r_work: 0.3047 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7972 Z= 0.121 Angle : 0.465 5.555 10752 Z= 0.240 Chirality : 0.035 0.123 1264 Planarity : 0.005 0.048 1264 Dihedral : 12.094 75.829 1260 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.65 % Allowed : 12.18 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.28), residues: 924 helix: 2.31 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.22 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.005 0.001 TYR C 270 PHE 0.017 0.001 PHE C 244 TRP 0.006 0.001 TRP C 365 HIS 0.001 0.000 HIS C 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 7972) covalent geometry : angle 0.46494 / 0.24 (10752) hydrogen bonds : bond 0.03545 / 2.36 ( 564) hydrogen bonds : angle 3.80313 / 2.62 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.416 Fit side-chains REVERT: A 356 LYS cc_start: 0.9099 (mttt) cc_final: 0.8811 (mttm) REVERT: A 378 ASP cc_start: 0.9235 (p0) cc_final: 0.8965 (p0) REVERT: B 356 LYS cc_start: 0.9077 (mttt) cc_final: 0.8801 (mttm) REVERT: B 378 ASP cc_start: 0.9241 (p0) cc_final: 0.8924 (p0) REVERT: C 356 LYS cc_start: 0.9101 (mttt) cc_final: 0.8811 (mttm) REVERT: C 378 ASP cc_start: 0.9234 (p0) cc_final: 0.8949 (p0) REVERT: D 356 LYS cc_start: 0.9077 (mttt) cc_final: 0.8799 (mttm) REVERT: D 378 ASP cc_start: 0.9225 (p0) cc_final: 0.8970 (p0) outliers start: 5 outliers final: 5 residues processed: 134 average time/residue: 0.8345 time to fit residues: 121.0628 Evaluate side-chains 137 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107912 restraints weight = 24003.090| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.96 r_work: 0.3055 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7972 Z= 0.106 Angle : 0.455 5.687 10752 Z= 0.235 Chirality : 0.035 0.123 1264 Planarity : 0.005 0.047 1264 Dihedral : 11.770 76.397 1260 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.17 % Allowed : 11.92 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.28), residues: 924 helix: 2.44 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.28 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 296 TYR 0.004 0.001 TYR A 270 PHE 0.016 0.001 PHE A 244 TRP 0.006 0.001 TRP B 365 HIS 0.001 0.000 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7972) covalent geometry : angle 0.45546 / 0.23 (10752) hydrogen bonds : bond 0.03345 / 2.22 ( 564) hydrogen bonds : angle 3.73633 / 2.57 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.395 Fit side-chains REVERT: A 356 LYS cc_start: 0.9102 (mttt) cc_final: 0.8820 (mttm) REVERT: A 378 ASP cc_start: 0.9229 (p0) cc_final: 0.8973 (p0) REVERT: B 356 LYS cc_start: 0.9083 (mttt) cc_final: 0.8812 (mttm) REVERT: B 378 ASP cc_start: 0.9225 (p0) cc_final: 0.8991 (p0) REVERT: C 356 LYS cc_start: 0.9076 (mttt) cc_final: 0.8800 (mttm) REVERT: C 378 ASP cc_start: 0.9223 (p0) cc_final: 0.8962 (p0) REVERT: D 356 LYS cc_start: 0.9074 (mttt) cc_final: 0.8800 (mttm) REVERT: D 378 ASP cc_start: 0.9226 (p0) cc_final: 0.8994 (p0) outliers start: 9 outliers final: 1 residues processed: 137 average time/residue: 0.8652 time to fit residues: 128.2356 Evaluate side-chains 135 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 371 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105641 restraints weight = 24246.842| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.99 r_work: 0.3023 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7972 Z= 0.141 Angle : 0.477 5.319 10752 Z= 0.249 Chirality : 0.035 0.121 1264 Planarity : 0.005 0.046 1264 Dihedral : 12.007 79.531 1260 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.52 % Allowed : 12.82 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.28), residues: 924 helix: 2.41 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.13 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 296 TYR 0.005 0.001 TYR D 270 PHE 0.016 0.001 PHE C 244 TRP 0.006 0.001 TRP A 365 HIS 0.002 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 7972) covalent geometry : angle 0.47708 / 0.25 (10752) hydrogen bonds : bond 0.03657 / 2.43 ( 564) hydrogen bonds : angle 3.80287 / 2.62 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4993.07 seconds wall clock time: 85 minutes 13.80 seconds (5113.80 seconds total)