Starting phenix.real_space_refine on Sat Aug 23 02:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpa_14852/08_2025/7zpa_14852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpa_14852/08_2025/7zpa_14852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpa_14852/08_2025/7zpa_14852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpa_14852/08_2025/7zpa_14852.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpa_14852/08_2025/7zpa_14852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpa_14852/08_2025/7zpa_14852.cif" } resolution = 3.9 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= 0.008 sd= 0.925 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 18 5.16 5 C 5544 2.51 5 N 1574 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3605 Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3636 Classifications: {'peptide': 443} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Time building chain proxies: 2.65, per 1000 atoms: 0.29 Number of scatterers: 9121 At special positions: 0 Unit cell: (83.566, 101.346, 136.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 97 15.00 O 1888 8.00 N 1574 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 355.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 46.5% alpha, 9.0% beta 12 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 4.480A pdb=" N TYR A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.592A pdb=" N VAL A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.779A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.545A pdb=" N GLY A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 4.366A pdb=" N THR A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.344A pdb=" N HIS A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.727A pdb=" N ARG A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.936A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 381 removed outlier: 4.065A pdb=" N LYS A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'B' and resid 15 through 31 removed outlier: 4.711A pdb=" N TYR B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 52 through 67 removed outlier: 3.601A pdb=" N VAL B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.876A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 190 removed outlier: 4.357A pdb=" N THR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.872A pdb=" N HIS B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.709A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 381 removed outlier: 3.804A pdb=" N LYS B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 450 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.991A pdb=" N GLY A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.618A pdb=" N TYR A 107 " --> pdb=" O LYS A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.609A pdb=" N GLY A 175 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 273 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 304 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU A 275 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP A 276 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR A 241 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 194 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR A 240 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 196 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 195 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE A 219 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 197 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.815A pdb=" N LEU A 388 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 401 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 440 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR A 423 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.592A pdb=" N GLY B 175 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.285A pdb=" N VAL B 194 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TYR B 240 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 196 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 239 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP B 276 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B 241 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.643A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 401 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 440 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2305 1.33 - 1.45: 2293 1.45 - 1.57: 4711 1.57 - 1.69: 190 1.69 - 1.81: 32 Bond restraints: 9531 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.542 0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.546 0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C4 LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.464 1.614 -0.150 2.00e-02 2.50e+03 5.61e+01 ... (remaining 9526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 13138 2.47 - 4.94: 155 4.94 - 7.40: 17 7.40 - 9.87: 3 9.87 - 12.34: 3 Bond angle restraints: 13316 Sorted by residual: angle pdb=" N VAL B 297 " pdb=" CA VAL B 297 " pdb=" C VAL B 297 " ideal model delta sigma weight residual 113.53 107.41 6.12 9.80e-01 1.04e+00 3.89e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.09 107.75 12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C GLU B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 122.69 116.68 6.01 1.59e+00 3.96e-01 1.43e+01 angle pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " pdb=" C4 LLP A 309 " ideal model delta sigma weight residual 120.09 109.00 11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CA ARG B 316 " pdb=" C ARG B 316 " pdb=" O ARG B 316 " ideal model delta sigma weight residual 122.44 117.71 4.73 1.32e+00 5.74e-01 1.28e+01 ... (remaining 13311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.53: 4922 27.53 - 55.07: 486 55.07 - 82.60: 55 82.60 - 110.14: 5 110.14 - 137.67: 1 Dihedral angle restraints: 5469 sinusoidal: 2885 harmonic: 2584 Sorted by residual: dihedral pdb=" CA ARG A 74 " pdb=" C ARG A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLU B 83 " pdb=" C GLU B 83 " pdb=" N ASP B 84 " pdb=" CA ASP B 84 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DA D 33 " pdb=" C3' DA D 33 " pdb=" O3' DA D 33 " pdb=" P DA D 34 " ideal model delta sinusoidal sigma weight residual 220.00 82.33 137.67 1 3.50e+01 8.16e-04 1.36e+01 ... (remaining 5466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 980 0.032 - 0.064: 321 0.064 - 0.097: 103 0.097 - 0.129: 49 0.129 - 0.161: 8 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CB ILE B 273 " pdb=" CA ILE B 273 " pdb=" CG1 ILE B 273 " pdb=" CG2 ILE B 273 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA GLU B 154 " pdb=" N GLU B 154 " pdb=" C GLU B 154 " pdb=" CB GLU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB VAL A 315 " pdb=" CA VAL A 315 " pdb=" CG1 VAL A 315 " pdb=" CG2 VAL A 315 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1458 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.159 2.00e-02 2.50e+03 2.67e-01 7.10e+02 pdb=" NZ LLP A 309 " -0.359 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.335 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " 0.078 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" NZ LLP B 309 " -0.082 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " 0.070 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 247 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 248 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.024 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1177 2.75 - 3.29: 8854 3.29 - 3.83: 15249 3.83 - 4.36: 16908 4.36 - 4.90: 27536 Nonbonded interactions: 69724 Sorted by model distance: nonbonded pdb=" OG1 THR B 168 " pdb=" OE1 GLN B 171 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 308 " pdb=" O ILE A 312 " model vdw 2.221 3.040 nonbonded pdb=" OE1 GLN B 184 " pdb=" OH TYR B 330 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 240 " pdb=" OD2 ASP B 276 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 162 " pdb=" OE2 GLU B 281 " model vdw 2.284 3.040 ... (remaining 69719 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 15 through 81 or resid 103 through 442 or resid 444 throug \ h 464)) selection = (chain 'B' and (resid 15 through 81 or resid 84 or resid 104 through 442 or resi \ d 444 through 464)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.150 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.006 0.184 9531 Z= 0.290 Angle : 0.698 12.341 13316 Z= 0.377 Chirality : 0.040 0.161 1461 Planarity : 0.009 0.267 1363 Dihedral : 19.492 137.671 3815 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.40 (0.29), residues: 861 helix: 0.90 (0.28), residues: 370 sheet: -0.29 (0.50), residues: 107 loop : -1.43 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 316 TYR 0.018 0.002 TYR A 337 PHE 0.020 0.002 PHE A 128 TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 9531) covalent geometry : angle 0.69764 (13316) hydrogen bonds : bond 0.16407 ( 309) hydrogen bonds : angle 7.02334 ( 866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7443 (ttm-80) REVERT: A 291 SER cc_start: 0.7372 (m) cc_final: 0.7086 (m) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0754 time to fit residues: 9.7476 Evaluate side-chains 66 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.119456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094356 restraints weight = 21429.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096359 restraints weight = 12704.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097749 restraints weight = 8704.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098701 restraints weight = 6639.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099343 restraints weight = 5504.677| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9531 Z= 0.165 Angle : 0.644 7.733 13316 Z= 0.357 Chirality : 0.042 0.156 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.461 138.388 2059 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.68 % Allowed : 8.39 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.44 (0.28), residues: 861 helix: 0.92 (0.27), residues: 376 sheet: -0.61 (0.47), residues: 112 loop : -1.44 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.024 0.002 TYR B 21 PHE 0.015 0.002 PHE A 352 TRP 0.010 0.001 TRP A 264 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9531) covalent geometry : angle 0.64390 (13316) hydrogen bonds : bond 0.05786 ( 309) hydrogen bonds : angle 4.47307 ( 866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.230 Fit side-chains REVERT: A 32 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7406 (ttm-80) REVERT: A 291 SER cc_start: 0.7212 (m) cc_final: 0.6938 (m) REVERT: A 413 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7749 (tp30) outliers start: 13 outliers final: 8 residues processed: 80 average time/residue: 0.0771 time to fit residues: 8.6897 Evaluate side-chains 74 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.119770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094180 restraints weight = 21189.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096254 restraints weight = 12512.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097723 restraints weight = 8505.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098707 restraints weight = 6427.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099319 restraints weight = 5318.583| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9531 Z= 0.155 Angle : 0.604 7.527 13316 Z= 0.338 Chirality : 0.041 0.157 1461 Planarity : 0.005 0.050 1363 Dihedral : 21.582 140.414 2059 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.55 % Allowed : 11.48 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.34 (0.29), residues: 861 helix: 1.04 (0.27), residues: 376 sheet: -0.72 (0.47), residues: 114 loop : -1.38 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.018 0.001 TYR B 21 PHE 0.012 0.002 PHE A 128 TRP 0.013 0.001 TRP A 124 HIS 0.007 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9531) covalent geometry : angle 0.60434 (13316) hydrogen bonds : bond 0.05098 ( 309) hydrogen bonds : angle 4.17981 ( 866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.227 Fit side-chains REVERT: A 291 SER cc_start: 0.7326 (m) cc_final: 0.7044 (m) REVERT: A 365 MET cc_start: 0.6184 (mmm) cc_final: 0.5861 (mmm) REVERT: B 115 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.5995 (m-30) REVERT: B 312 ILE cc_start: 0.7820 (mm) cc_final: 0.7529 (tp) outliers start: 12 outliers final: 7 residues processed: 80 average time/residue: 0.0690 time to fit residues: 8.2789 Evaluate side-chains 76 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 353 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 57 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN B 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097684 restraints weight = 20981.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099932 restraints weight = 11979.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101460 restraints weight = 7940.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102478 restraints weight = 5911.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103025 restraints weight = 4852.699| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9531 Z= 0.125 Angle : 0.560 8.291 13316 Z= 0.313 Chirality : 0.039 0.143 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.547 141.489 2059 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.29 % Allowed : 14.32 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.11 (0.29), residues: 861 helix: 1.28 (0.28), residues: 377 sheet: -0.63 (0.47), residues: 114 loop : -1.31 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.020 0.001 TYR B 21 PHE 0.011 0.001 PHE A 77 TRP 0.015 0.001 TRP A 124 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9531) covalent geometry : angle 0.56034 (13316) hydrogen bonds : bond 0.04331 ( 309) hydrogen bonds : angle 3.89912 ( 866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.5979 (mmm) cc_final: 0.5668 (mmm) REVERT: A 413 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7804 (tp30) REVERT: B 38 LYS cc_start: 0.7418 (mmtt) cc_final: 0.6889 (tptt) REVERT: B 115 ASP cc_start: 0.6329 (m-30) cc_final: 0.6074 (m-30) REVERT: B 365 MET cc_start: 0.8392 (mmm) cc_final: 0.7981 (mmm) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 0.0728 time to fit residues: 9.2020 Evaluate side-chains 77 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 142 ASN B 142 ASN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.122621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097007 restraints weight = 21004.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.099176 restraints weight = 12149.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.100668 restraints weight = 8143.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.101691 restraints weight = 6118.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102198 restraints weight = 5007.399| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9531 Z= 0.127 Angle : 0.560 8.326 13316 Z= 0.311 Chirality : 0.039 0.146 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.644 142.189 2059 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.94 % Allowed : 16.00 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.03 (0.29), residues: 861 helix: 1.32 (0.28), residues: 378 sheet: -0.38 (0.48), residues: 108 loop : -1.33 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.020 0.001 TYR B 21 PHE 0.010 0.001 PHE A 77 TRP 0.014 0.001 TRP A 124 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9531) covalent geometry : angle 0.56014 (13316) hydrogen bonds : bond 0.04233 ( 309) hydrogen bonds : angle 3.81440 ( 866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.187 Fit side-chains REVERT: A 365 MET cc_start: 0.6015 (mmm) cc_final: 0.5615 (mmm) REVERT: A 413 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7861 (tp30) REVERT: B 38 LYS cc_start: 0.7389 (mmtt) cc_final: 0.6808 (tptt) REVERT: B 115 ASP cc_start: 0.6279 (m-30) cc_final: 0.6007 (m-30) REVERT: B 312 ILE cc_start: 0.7803 (mm) cc_final: 0.7473 (tp) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.0747 time to fit residues: 9.3581 Evaluate side-chains 79 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097270 restraints weight = 20911.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099434 restraints weight = 12108.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100932 restraints weight = 8125.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101938 restraints weight = 6110.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102560 restraints weight = 5018.565| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9531 Z= 0.125 Angle : 0.557 8.400 13316 Z= 0.309 Chirality : 0.039 0.220 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.679 142.147 2059 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.55 % Allowed : 16.77 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.07 (0.29), residues: 861 helix: 1.40 (0.28), residues: 377 sheet: -0.26 (0.48), residues: 109 loop : -1.28 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.020 0.001 TYR A 336 PHE 0.010 0.001 PHE A 77 TRP 0.014 0.001 TRP A 124 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9531) covalent geometry : angle 0.55705 (13316) hydrogen bonds : bond 0.04148 ( 309) hydrogen bonds : angle 3.75236 ( 866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.284 Fit side-chains REVERT: A 312 ILE cc_start: 0.8695 (mp) cc_final: 0.8420 (mp) REVERT: A 365 MET cc_start: 0.5979 (mmm) cc_final: 0.5694 (mmm) REVERT: A 413 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7810 (tp30) REVERT: B 38 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6796 (tptt) REVERT: B 115 ASP cc_start: 0.6327 (m-30) cc_final: 0.6084 (m-30) REVERT: B 153 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6877 (ttp-170) REVERT: B 339 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8161 (t) REVERT: B 365 MET cc_start: 0.8457 (mmm) cc_final: 0.7997 (mmm) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.0773 time to fit residues: 9.3932 Evaluate side-chains 78 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 8 optimal weight: 0.1980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.123745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098073 restraints weight = 20941.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100294 restraints weight = 12017.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101805 restraints weight = 8014.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.102798 restraints weight = 6003.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103431 restraints weight = 4929.712| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9531 Z= 0.122 Angle : 0.554 8.252 13316 Z= 0.305 Chirality : 0.039 0.189 1461 Planarity : 0.004 0.048 1363 Dihedral : 21.705 141.964 2059 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.42 % Allowed : 17.81 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.15 (0.29), residues: 861 helix: 1.47 (0.28), residues: 377 sheet: -0.30 (0.48), residues: 115 loop : -1.22 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.020 0.001 TYR B 21 PHE 0.011 0.001 PHE A 119 TRP 0.016 0.001 TRP A 124 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9531) covalent geometry : angle 0.55409 (13316) hydrogen bonds : bond 0.04088 ( 309) hydrogen bonds : angle 3.68144 ( 866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.220 Fit side-chains REVERT: A 44 LYS cc_start: 0.7891 (tttp) cc_final: 0.7550 (mtmt) REVERT: A 365 MET cc_start: 0.6015 (mmm) cc_final: 0.5717 (mmm) REVERT: A 403 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7039 (mttp) REVERT: A 413 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7835 (tp30) REVERT: B 38 LYS cc_start: 0.7376 (mmtt) cc_final: 0.6787 (tptt) REVERT: B 61 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7608 (mt-10) REVERT: B 115 ASP cc_start: 0.6317 (m-30) cc_final: 0.6056 (m-30) REVERT: B 153 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6858 (ttp-170) REVERT: B 339 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8093 (t) REVERT: B 365 MET cc_start: 0.8416 (mmm) cc_final: 0.7941 (mmm) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.0850 time to fit residues: 9.9299 Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.124158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098508 restraints weight = 20660.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.100696 restraints weight = 11868.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102227 restraints weight = 7921.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103239 restraints weight = 5914.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103841 restraints weight = 4856.442| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9531 Z= 0.120 Angle : 0.552 7.941 13316 Z= 0.303 Chirality : 0.039 0.177 1461 Planarity : 0.004 0.047 1363 Dihedral : 21.753 141.793 2059 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.81 % Allowed : 17.68 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.21 (0.29), residues: 861 helix: 1.54 (0.28), residues: 377 sheet: -0.24 (0.48), residues: 115 loop : -1.23 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 138 TYR 0.020 0.001 TYR B 21 PHE 0.019 0.001 PHE A 119 TRP 0.017 0.001 TRP A 124 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9531) covalent geometry : angle 0.55198 (13316) hydrogen bonds : bond 0.04054 ( 309) hydrogen bonds : angle 3.66879 ( 866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.310 Fit side-chains REVERT: A 44 LYS cc_start: 0.7881 (tttp) cc_final: 0.7537 (mtmt) REVERT: A 307 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7425 (t80) REVERT: A 365 MET cc_start: 0.6011 (mmm) cc_final: 0.5740 (mmm) REVERT: A 403 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7025 (mttp) REVERT: A 413 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7864 (tp30) REVERT: B 38 LYS cc_start: 0.7360 (mmtt) cc_final: 0.6735 (tptt) REVERT: B 115 ASP cc_start: 0.6356 (m-30) cc_final: 0.6086 (m-30) REVERT: B 153 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6872 (ttp-170) REVERT: B 339 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8045 (t) REVERT: B 365 MET cc_start: 0.8452 (mmm) cc_final: 0.8008 (mmm) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.0720 time to fit residues: 8.5973 Evaluate side-chains 81 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.123402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097707 restraints weight = 20801.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099876 restraints weight = 12069.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101387 restraints weight = 8100.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102396 restraints weight = 6066.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102933 restraints weight = 4978.010| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9531 Z= 0.129 Angle : 0.581 12.199 13316 Z= 0.312 Chirality : 0.039 0.176 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.825 141.430 2059 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.68 % Allowed : 18.06 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.20 (0.29), residues: 861 helix: 1.53 (0.28), residues: 377 sheet: -0.30 (0.47), residues: 115 loop : -1.21 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.022 0.001 TYR B 21 PHE 0.010 0.001 PHE B 186 TRP 0.025 0.002 TRP A 124 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9531) covalent geometry : angle 0.58074 (13316) hydrogen bonds : bond 0.04091 ( 309) hydrogen bonds : angle 3.75788 ( 866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.256 Fit side-chains REVERT: A 44 LYS cc_start: 0.7890 (tttp) cc_final: 0.7553 (mtmt) REVERT: A 307 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7429 (t80) REVERT: A 403 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7029 (mttp) REVERT: A 413 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7845 (tp30) REVERT: B 38 LYS cc_start: 0.7417 (mmtt) cc_final: 0.6772 (tptt) REVERT: B 61 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7652 (mt-10) REVERT: B 115 ASP cc_start: 0.6291 (m-30) cc_final: 0.5969 (m-30) REVERT: B 153 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6903 (ttp-170) REVERT: B 339 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.7957 (t) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.0923 time to fit residues: 10.5877 Evaluate side-chains 81 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 91 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 54 optimal weight: 0.0980 chunk 47 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 146 GLN A 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.123700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097946 restraints weight = 20665.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100136 restraints weight = 11996.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101617 restraints weight = 8044.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.102630 restraints weight = 6052.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103240 restraints weight = 4968.697| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9531 Z= 0.127 Angle : 0.578 12.001 13316 Z= 0.311 Chirality : 0.039 0.194 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.851 141.189 2059 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.94 % Allowed : 17.94 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.21 (0.29), residues: 861 helix: 1.53 (0.28), residues: 377 sheet: -0.26 (0.47), residues: 115 loop : -1.21 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.022 0.001 TYR B 21 PHE 0.013 0.001 PHE B 186 TRP 0.034 0.002 TRP A 124 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9531) covalent geometry : angle 0.57813 (13316) hydrogen bonds : bond 0.04089 ( 309) hydrogen bonds : angle 3.75645 ( 866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.281 Fit side-chains REVERT: A 44 LYS cc_start: 0.7892 (tttp) cc_final: 0.7557 (mtmt) REVERT: A 307 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7327 (t80) REVERT: A 403 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7034 (mttp) REVERT: A 413 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7844 (tp30) REVERT: B 38 LYS cc_start: 0.7411 (mmtt) cc_final: 0.6776 (tptt) REVERT: B 61 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7639 (mt-10) REVERT: B 115 ASP cc_start: 0.6221 (m-30) cc_final: 0.5949 (m-30) REVERT: B 153 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6907 (ttp-170) REVERT: B 339 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.7982 (t) REVERT: B 365 MET cc_start: 0.8461 (mmm) cc_final: 0.7924 (mmm) REVERT: B 409 GLN cc_start: 0.8316 (mm110) cc_final: 0.7959 (mm-40) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.0848 time to fit residues: 10.1286 Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.123484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097876 restraints weight = 20546.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100005 restraints weight = 11918.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101472 restraints weight = 8061.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102471 restraints weight = 6068.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102996 restraints weight = 4982.546| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 9531 Z= 0.157 Angle : 0.866 59.195 13316 Z= 0.505 Chirality : 0.042 0.535 1461 Planarity : 0.005 0.053 1363 Dihedral : 21.856 141.149 2059 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.42 % Rotamer: Outliers : 1.81 % Allowed : 18.45 % Favored : 79.74 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.20 (0.29), residues: 861 helix: 1.52 (0.28), residues: 377 sheet: -0.27 (0.47), residues: 115 loop : -1.22 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 138 TYR 0.021 0.001 TYR A 336 PHE 0.011 0.001 PHE B 186 TRP 0.030 0.002 TRP A 124 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9531) covalent geometry : angle 0.86579 (13316) hydrogen bonds : bond 0.04096 ( 309) hydrogen bonds : angle 3.75738 ( 866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1575.55 seconds wall clock time: 27 minutes 46.12 seconds (1666.12 seconds total)