Starting phenix.real_space_refine on Sat Oct 24 18:22:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y71_72638/10_2026/9y71_72638.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y71_72638/10_2026/9y71_72638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y71_72638/10_2026/9y71_72638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y71_72638/10_2026/9y71_72638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y71_72638/10_2026/9y71_72638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y71_72638/10_2026/9y71_72638.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9168 2.51 5 N 2228 2.21 5 O 2480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13968 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3465 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 5, 'TRANS': 419} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.72, per 1000 atoms: 0.19 Number of scatterers: 13968 At special positions: 0 Unit cell: (105.002, 105.002, 112.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2480 8.00 N 2228 7.00 C 9168 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: 0.95 Conformation dependent library (CDL) restraints added in 609.2 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 68.3% alpha, 18.4% 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 39 through 48 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.734A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 292 through 324 Processing helix chain 'A' and resid 347 through 371 Processing helix chain 'A' and resid 375 through 398 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 413 through 439 Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.627A pdb=" N PHE A 446 " --> pdb=" O HIS A 443 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 443 through 447' Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 476 through 511 Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.735A pdb=" N VAL B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 292 through 324 Processing helix chain 'B' and resid 347 through 371 Processing helix chain 'B' and resid 375 through 398 Processing helix chain 'B' and resid 400 through 413 Processing helix chain 'B' and resid 413 through 439 Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.626A pdb=" N PHE B 446 " --> pdb=" O HIS B 443 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 443 through 447' Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 476 through 511 Processing helix chain 'C' and resid 40 through 48 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.734A pdb=" N VAL C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 140 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 292 through 324 Processing helix chain 'C' and resid 347 through 371 Processing helix chain 'C' and resid 375 through 398 Processing helix chain 'C' and resid 400 through 413 Processing helix chain 'C' and resid 413 through 439 Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.627A pdb=" N PHE C 446 " --> pdb=" O HIS C 443 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 443 through 447' Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 511 Processing helix chain 'D' and resid 40 through 48 Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.734A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 195 through 199 Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 292 through 324 Processing helix chain 'D' and resid 347 through 371 Processing helix chain 'D' and resid 375 through 398 Processing helix chain 'D' and resid 400 through 413 Processing helix chain 'D' and resid 413 through 439 Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.628A pdb=" N PHE D 446 " --> pdb=" O HIS D 443 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 443 through 447' Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 476 through 511 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.642A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS A 243 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.642A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS A 243 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 220 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA A 226 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 160 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.642A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS B 243 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.642A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS B 243 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 220 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA B 226 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 160 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.642A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS C 243 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.642A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS C 243 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 220 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA C 226 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY C 160 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.641A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS D 243 " --> pdb=" O GLU D 272 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.641A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS D 243 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 220 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA D 226 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY D 160 " --> pdb=" O ALA D 226 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3047 1.33 - 1.45: 3218 1.45 - 1.57: 7879 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 14272 Sorted by residual: bond pdb=" C10 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.367 1.442 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C10 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 1.367 1.442 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C10 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 1.367 1.442 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C10 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 1.367 1.442 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N LEU D 314 " pdb=" CA LEU D 314 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.38e+00 ... (remaining 14267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 19024 2.11 - 4.22: 220 4.22 - 6.32: 48 6.32 - 8.43: 20 8.43 - 10.54: 4 Bond angle restraints: 19316 Sorted by residual: angle pdb=" N LEU C 316 " pdb=" CA LEU C 316 " pdb=" C LEU C 316 " ideal model delta sigma weight residual 111.14 106.31 4.83 1.08e+00 8.57e-01 2.00e+01 angle pdb=" N LEU D 316 " pdb=" CA LEU D 316 " pdb=" C LEU D 316 " ideal model delta sigma weight residual 111.14 106.31 4.83 1.08e+00 8.57e-01 2.00e+01 angle pdb=" N LEU A 316 " pdb=" CA LEU A 316 " pdb=" C LEU A 316 " ideal model delta sigma weight residual 111.14 106.33 4.81 1.08e+00 8.57e-01 1.98e+01 angle pdb=" N LEU B 316 " pdb=" CA LEU B 316 " pdb=" C LEU B 316 " ideal model delta sigma weight residual 111.14 106.33 4.81 1.08e+00 8.57e-01 1.98e+01 angle pdb=" C21 AQV D 601 " pdb=" C11 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 110.51 121.05 -10.54 3.00e+00 1.11e-01 1.23e+01 ... (remaining 19311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 7226 15.22 - 30.44: 866 30.44 - 45.65: 272 45.65 - 60.87: 20 60.87 - 76.09: 24 Dihedral angle restraints: 8408 sinusoidal: 3388 harmonic: 5020 Sorted by residual: dihedral pdb=" CA MET A 50 " pdb=" C MET A 50 " pdb=" N SER A 51 " pdb=" CA SER A 51 " ideal model delta harmonic sigma weight residual 180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA MET C 50 " pdb=" C MET C 50 " pdb=" N SER C 51 " pdb=" CA SER C 51 " ideal model delta harmonic sigma weight residual 180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA MET D 50 " pdb=" C MET D 50 " pdb=" N SER D 51 " pdb=" CA SER D 51 " ideal model delta harmonic sigma weight residual 180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1852 0.053 - 0.106: 300 0.106 - 0.159: 52 0.159 - 0.212: 0 0.212 - 0.265: 16 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CA LEU D 314 " pdb=" N LEU D 314 " pdb=" C LEU D 314 " pdb=" CB LEU D 314 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU B 314 " pdb=" N LEU B 314 " pdb=" C LEU B 314 " pdb=" CB LEU B 314 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LEU C 314 " pdb=" N LEU C 314 " pdb=" C LEU C 314 " pdb=" CB LEU C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2217 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 494 " -0.017 2.00e-02 2.50e+03 1.51e-02 3.97e+00 pdb=" CG PHE B 494 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 494 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 494 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 494 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 494 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 494 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 494 " 0.017 2.00e-02 2.50e+03 1.49e-02 3.86e+00 pdb=" CG PHE C 494 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 494 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 494 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 494 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 494 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 494 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 494 " -0.017 2.00e-02 2.50e+03 1.49e-02 3.86e+00 pdb=" CG PHE A 494 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 494 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 494 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 494 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 494 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 494 " -0.001 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 135 2.67 - 3.23: 13396 3.23 - 3.79: 21275 3.79 - 4.34: 27878 4.34 - 4.90: 47183 Nonbonded interactions: 109867 Sorted by model distance: nonbonded pdb=" OH TYR A 428 " pdb=" O ALA A 453 " model vdw 2.115 3.040 nonbonded pdb=" OH TYR B 428 " pdb=" O ALA B 453 " model vdw 2.115 3.040 nonbonded pdb=" OH TYR D 428 " pdb=" O ALA D 453 " model vdw 2.115 3.040 nonbonded pdb=" OH TYR C 428 " pdb=" O ALA C 453 " model vdw 2.115 3.040 nonbonded pdb=" O TYR D 375 " pdb=" OG SER D 379 " model vdw 2.236 3.040 ... (remaining 109862 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.003 0.075 14272 Z= 0.173 Angle : 0.639 10.539 19316 Z= 0.345 Chirality : 0.044 0.265 2220 Planarity : 0.003 0.019 2344 Dihedral : 14.593 76.091 5160 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1660 helix: 1.86 (0.15), residues: 1072 sheet: -0.68 (0.36), residues: 220 loop : -0.09 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.011 0.001 TYR B 56 PHE 0.035 0.002 PHE B 494 TRP 0.008 0.001 TRP D 346 HIS 0.002 0.000 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (14272) covalent geometry : angle 0.63926 / 0.35 (19316) hydrogen bonds : bond 0.12066 / 7.61 ( 1013) hydrogen bonds : angle 5.98557 / 4.28 ( 3171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.532 Fit side-chains REVERT: A 375 TYR cc_start: 0.7615 (m-80) cc_final: 0.7400 (m-10) REVERT: B 496 TYR cc_start: 0.8596 (t80) cc_final: 0.8061 (t80) REVERT: D 82 ARG cc_start: 0.7285 (mmt180) cc_final: 0.7073 (mmt180) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1037 time to fit residues: 41.2293 Evaluate side-chains 207 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.208784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143654 restraints weight = 14921.759| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.46 r_work: 0.3374 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14272 Z= 0.138 Angle : 0.557 8.552 19316 Z= 0.290 Chirality : 0.039 0.161 2220 Planarity : 0.003 0.023 2344 Dihedral : 6.031 58.048 1932 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.17 % Allowed : 5.05 % Favored : 93.78 % 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: 1.89 (0.20), residues: 1660 helix: 2.12 (0.15), residues: 1072 sheet: -0.42 (0.35), residues: 220 loop : -0.16 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 395 TYR 0.015 0.001 TYR A 56 PHE 0.021 0.002 PHE D 293 TRP 0.013 0.001 TRP A 480 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (14272) covalent geometry : angle 0.55748 / 0.29 (19316) hydrogen bonds : bond 0.04565 / 2.98 ( 1013) hydrogen bonds : angle 4.26349 / 3.00 ( 3171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.451 Fit side-chains REVERT: A 319 ARG cc_start: 0.5398 (mtt90) cc_final: 0.5192 (ttm170) REVERT: A 480 TRP cc_start: 0.7959 (t60) cc_final: 0.7727 (t60) REVERT: B 365 MET cc_start: 0.8357 (ttt) cc_final: 0.8049 (ttp) REVERT: B 496 TYR cc_start: 0.8383 (t80) cc_final: 0.8025 (t80) REVERT: C 50 MET cc_start: 0.6919 (tmm) cc_final: 0.6541 (tmm) REVERT: C 365 MET cc_start: 0.8368 (ttt) cc_final: 0.8068 (ttp) REVERT: C 471 GLN cc_start: 0.8017 (mt0) cc_final: 0.7601 (mm-40) REVERT: C 477 ILE cc_start: 0.7845 (mm) cc_final: 0.7359 (tp) REVERT: C 481 LEU cc_start: 0.8720 (mp) cc_final: 0.8271 (mp) REVERT: D 50 MET cc_start: 0.6671 (tmm) cc_final: 0.6286 (tmm) REVERT: D 471 GLN cc_start: 0.7994 (mt0) cc_final: 0.7415 (mm-40) REVERT: D 477 ILE cc_start: 0.7766 (mm) cc_final: 0.7265 (tp) REVERT: D 481 LEU cc_start: 0.8805 (mp) cc_final: 0.8317 (mp) REVERT: D 496 TYR cc_start: 0.8257 (t80) cc_final: 0.8056 (t80) outliers start: 18 outliers final: 10 residues processed: 235 average time/residue: 0.1025 time to fit residues: 37.1943 Evaluate side-chains 217 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 193 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [133, 97, 59, 103, 109, 81, 90, 63, 167, 72, 74] chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.207123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140493 restraints weight = 15022.535| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.15 r_work: 0.3386 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14272 Z= 0.149 Angle : 0.538 7.703 19316 Z= 0.283 Chirality : 0.040 0.284 2220 Planarity : 0.003 0.024 2344 Dihedral : 5.874 56.749 1932 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.75 % Allowed : 7.32 % Favored : 90.93 % 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: 1.92 (0.20), residues: 1660 helix: 2.13 (0.15), residues: 1072 sheet: -0.32 (0.34), residues: 220 loop : -0.18 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 395 TYR 0.013 0.001 TYR A 56 PHE 0.021 0.002 PHE C 502 TRP 0.012 0.001 TRP B 480 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14272) covalent geometry : angle 0.53815 / 0.28 (19316) hydrogen bonds : bond 0.04533 / 2.97 ( 1013) hydrogen bonds : angle 4.11871 / 2.90 ( 3171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.555 Fit side-chains REVERT: A 319 ARG cc_start: 0.5485 (mtt90) cc_final: 0.5244 (ttm170) REVERT: A 480 TRP cc_start: 0.7908 (t60) cc_final: 0.7587 (t60) REVERT: B 365 MET cc_start: 0.8551 (ttt) cc_final: 0.8200 (ttp) REVERT: B 496 TYR cc_start: 0.8339 (t80) cc_final: 0.8017 (t80) REVERT: C 50 MET cc_start: 0.6924 (tmm) cc_final: 0.6697 (tmm) REVERT: C 365 MET cc_start: 0.8510 (ttt) cc_final: 0.8199 (ttp) REVERT: C 444 GLU cc_start: 0.8073 (mp0) cc_final: 0.7763 (mp0) REVERT: C 471 GLN cc_start: 0.8116 (mt0) cc_final: 0.7609 (mm-40) REVERT: C 477 ILE cc_start: 0.7871 (mm) cc_final: 0.7181 (tp) REVERT: C 481 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8171 (mp) REVERT: D 371 LYS cc_start: 0.7209 (mmmt) cc_final: 0.5781 (pttp) REVERT: D 477 ILE cc_start: 0.7817 (mm) cc_final: 0.7169 (tp) REVERT: D 481 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8311 (mp) REVERT: D 496 TYR cc_start: 0.8180 (t80) cc_final: 0.7974 (t80) outliers start: 27 outliers final: 17 residues processed: 229 average time/residue: 0.0984 time to fit residues: 34.9955 Evaluate side-chains 218 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [119, 156, 2, 70, 135, 53, 43, 12, 120, 16, 57] chunk 119 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.206117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143570 restraints weight = 15138.124| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.05 r_work: 0.3406 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14272 Z= 0.142 Angle : 0.531 8.131 19316 Z= 0.279 Chirality : 0.039 0.231 2220 Planarity : 0.003 0.023 2344 Dihedral : 5.797 56.125 1932 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.20 % Allowed : 9.72 % Favored : 88.08 % 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: 1.96 (0.20), residues: 1660 helix: 2.14 (0.15), residues: 1072 sheet: -0.26 (0.34), residues: 220 loop : -0.11 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 395 TYR 0.013 0.001 TYR A 56 PHE 0.024 0.002 PHE C 502 TRP 0.013 0.001 TRP B 480 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14272) covalent geometry : angle 0.53135 / 0.28 (19316) hydrogen bonds : bond 0.04443 / 2.92 ( 1013) hydrogen bonds : angle 4.04310 / 2.85 ( 3171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.427 Fit side-chains REVERT: B 365 MET cc_start: 0.8291 (ttt) cc_final: 0.7961 (ttp) REVERT: B 496 TYR cc_start: 0.8475 (t80) cc_final: 0.8143 (t80) REVERT: C 363 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7967 (tt) REVERT: C 365 MET cc_start: 0.8192 (ttt) cc_final: 0.7921 (ttp) REVERT: C 444 GLU cc_start: 0.7851 (mp0) cc_final: 0.7604 (mp0) REVERT: C 477 ILE cc_start: 0.7942 (mm) cc_final: 0.7279 (tp) REVERT: C 481 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8176 (mp) REVERT: D 363 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8154 (tt) REVERT: D 371 LYS cc_start: 0.7321 (mmmt) cc_final: 0.6010 (pttp) REVERT: D 477 ILE cc_start: 0.7854 (mm) cc_final: 0.7127 (tp) REVERT: D 481 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8245 (mp) REVERT: D 496 TYR cc_start: 0.8262 (t80) cc_final: 0.8048 (t80) outliers start: 34 outliers final: 18 residues processed: 232 average time/residue: 0.1036 time to fit residues: 36.9576 Evaluate side-chains 225 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [32, 142, 80, 49, 141, 79, 33, 127, 40, 4, 110] chunk 32 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.203228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140721 restraints weight = 15235.826| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.35 r_work: 0.3343 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14272 Z= 0.180 Angle : 0.563 8.654 19316 Z= 0.297 Chirality : 0.041 0.297 2220 Planarity : 0.003 0.022 2344 Dihedral : 5.961 57.327 1932 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.46 % Allowed : 11.14 % Favored : 86.40 % 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: 1.81 (0.20), residues: 1660 helix: 2.00 (0.15), residues: 1072 sheet: -0.20 (0.34), residues: 220 loop : -0.17 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.013 0.001 TYR C 56 PHE 0.026 0.002 PHE C 502 TRP 0.015 0.001 TRP B 346 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (14272) covalent geometry : angle 0.56289 / 0.30 (19316) hydrogen bonds : bond 0.04699 / 3.09 ( 1013) hydrogen bonds : angle 4.15424 / 2.92 ( 3171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.609 Fit side-chains REVERT: A 50 MET cc_start: 0.6373 (ppp) cc_final: 0.6097 (ppp) REVERT: B 365 MET cc_start: 0.8302 (ttt) cc_final: 0.7952 (ttp) REVERT: B 496 TYR cc_start: 0.8527 (t80) cc_final: 0.8228 (t80) REVERT: C 363 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 365 MET cc_start: 0.8318 (ttt) cc_final: 0.7998 (ttp) REVERT: C 444 GLU cc_start: 0.7877 (mp0) cc_final: 0.7618 (mp0) REVERT: C 477 ILE cc_start: 0.7955 (mm) cc_final: 0.7446 (tp) REVERT: C 481 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 496 TYR cc_start: 0.8325 (t80) cc_final: 0.8094 (t80) REVERT: D 363 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8146 (tt) REVERT: D 371 LYS cc_start: 0.7316 (mmmt) cc_final: 0.6049 (pttp) REVERT: D 477 ILE cc_start: 0.7873 (mm) cc_final: 0.7094 (tp) REVERT: D 481 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8237 (mp) REVERT: D 496 TYR cc_start: 0.8350 (t80) cc_final: 0.8134 (t80) outliers start: 38 outliers final: 21 residues processed: 237 average time/residue: 0.0954 time to fit residues: 35.2185 Evaluate side-chains 228 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [27, 166, 92, 142, 131, 19, 99, 34, 94, 57, 49] chunk 27 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 142 optimal weight: 0.0980 chunk 131 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.206914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141675 restraints weight = 15098.682| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.07 r_work: 0.3412 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14272 Z= 0.124 Angle : 0.530 9.615 19316 Z= 0.273 Chirality : 0.038 0.209 2220 Planarity : 0.002 0.021 2344 Dihedral : 5.631 55.475 1932 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.40 % Allowed : 12.05 % Favored : 85.56 % 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: 1.97 (0.20), residues: 1660 helix: 2.11 (0.15), residues: 1072 sheet: -0.18 (0.34), residues: 220 loop : -0.02 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.012 0.001 TYR D 442 PHE 0.032 0.001 PHE B 502 TRP 0.013 0.001 TRP D 346 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14272) covalent geometry : angle 0.53021 / 0.27 (19316) hydrogen bonds : bond 0.04305 / 2.84 ( 1013) hydrogen bonds : angle 3.95391 / 2.78 ( 3171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.398 Fit side-chains REVERT: A 50 MET cc_start: 0.6735 (ppp) cc_final: 0.6482 (ppp) REVERT: B 50 MET cc_start: 0.7085 (ppp) cc_final: 0.6884 (tmm) REVERT: B 365 MET cc_start: 0.8391 (ttt) cc_final: 0.8031 (ttp) REVERT: B 496 TYR cc_start: 0.8328 (t80) cc_final: 0.8059 (t80) REVERT: C 363 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8031 (tt) REVERT: C 365 MET cc_start: 0.8406 (ttt) cc_final: 0.8069 (ttp) REVERT: C 444 GLU cc_start: 0.8051 (mp0) cc_final: 0.7771 (mp0) REVERT: C 477 ILE cc_start: 0.7864 (mm) cc_final: 0.7130 (tp) REVERT: C 481 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8168 (mp) REVERT: D 371 LYS cc_start: 0.7219 (mmmt) cc_final: 0.5941 (pttp) REVERT: D 444 GLU cc_start: 0.7999 (mp0) cc_final: 0.7727 (mp0) REVERT: D 477 ILE cc_start: 0.7828 (mm) cc_final: 0.7005 (tp) REVERT: D 481 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8233 (mp) REVERT: D 496 TYR cc_start: 0.8086 (t80) cc_final: 0.7860 (t80) outliers start: 37 outliers final: 24 residues processed: 232 average time/residue: 0.0967 time to fit residues: 34.8007 Evaluate side-chains 225 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [105, 111, 89, 124, 127, 154, 66, 54, 56, 83, 30] chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.201841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140339 restraints weight = 15229.831| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.25 r_work: 0.3310 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14272 Z= 0.210 Angle : 0.600 12.267 19316 Z= 0.314 Chirality : 0.041 0.168 2220 Planarity : 0.003 0.021 2344 Dihedral : 6.070 58.153 1932 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 12.95 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.20), residues: 1660 helix: 1.92 (0.15), residues: 1072 sheet: -0.18 (0.34), residues: 220 loop : -0.13 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 419 TYR 0.014 0.002 TYR A 496 PHE 0.031 0.002 PHE A 502 TRP 0.016 0.002 TRP B 346 HIS 0.003 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (14272) covalent geometry : angle 0.60039 / 0.31 (19316) hydrogen bonds : bond 0.04881 / 3.21 ( 1013) hydrogen bonds : angle 4.23777 / 2.98 ( 3171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.534 Fit side-chains REVERT: A 50 MET cc_start: 0.6805 (ppp) cc_final: 0.6521 (ppp) REVERT: B 365 MET cc_start: 0.8291 (ttt) cc_final: 0.7957 (ttp) REVERT: B 496 TYR cc_start: 0.8528 (t80) cc_final: 0.8253 (t80) REVERT: C 363 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7991 (tt) REVERT: C 444 GLU cc_start: 0.7841 (mp0) cc_final: 0.7585 (mp0) REVERT: C 477 ILE cc_start: 0.7956 (mm) cc_final: 0.7429 (tp) REVERT: C 481 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 496 TYR cc_start: 0.8512 (t80) cc_final: 0.8289 (t80) REVERT: D 363 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8061 (tt) REVERT: D 477 ILE cc_start: 0.7926 (mm) cc_final: 0.7283 (tp) REVERT: D 481 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8367 (mp) outliers start: 39 outliers final: 32 residues processed: 231 average time/residue: 0.0974 time to fit residues: 35.1007 Evaluate side-chains 235 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [78, 136, 158, 153, 11, 104, 114, 133, 29, 55, 83] chunk 78 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 chunk 158 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.206242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141858 restraints weight = 15277.731| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.46 r_work: 0.3277 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14272 Z= 0.127 Angle : 0.555 14.715 19316 Z= 0.282 Chirality : 0.038 0.159 2220 Planarity : 0.003 0.021 2344 Dihedral : 5.627 55.654 1932 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.40 % Allowed : 13.99 % Favored : 83.61 % 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: 1.97 (0.20), residues: 1660 helix: 2.10 (0.15), residues: 1072 sheet: -0.15 (0.34), residues: 220 loop : -0.04 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 419 TYR 0.012 0.001 TYR C 56 PHE 0.035 0.001 PHE A 502 TRP 0.016 0.001 TRP B 480 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (14272) covalent geometry : angle 0.55525 / 0.28 (19316) hydrogen bonds : bond 0.04348 / 2.87 ( 1013) hydrogen bonds : angle 4.00048 / 2.81 ( 3171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.503 Fit side-chains REVERT: A 50 MET cc_start: 0.6833 (ppp) cc_final: 0.6525 (ppp) REVERT: B 365 MET cc_start: 0.8329 (ttt) cc_final: 0.7974 (ttp) REVERT: B 496 TYR cc_start: 0.8384 (t80) cc_final: 0.8118 (t80) REVERT: C 363 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7986 (tt) REVERT: C 444 GLU cc_start: 0.7891 (mp0) cc_final: 0.7622 (mp0) REVERT: C 477 ILE cc_start: 0.7830 (mm) cc_final: 0.7091 (tp) REVERT: C 481 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8192 (mp) REVERT: C 496 TYR cc_start: 0.8323 (t80) cc_final: 0.8117 (t80) REVERT: D 363 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7960 (tt) REVERT: D 444 GLU cc_start: 0.7853 (mp0) cc_final: 0.7581 (mp0) REVERT: D 477 ILE cc_start: 0.7780 (mm) cc_final: 0.6975 (tp) REVERT: D 481 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8183 (mp) outliers start: 37 outliers final: 26 residues processed: 229 average time/residue: 0.0986 time to fit residues: 35.1123 Evaluate side-chains 225 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [3, 45, 159, 93, 79, 110, 128, 19, 150, 23, 123] chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.205813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139272 restraints weight = 15257.740| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.15 r_work: 0.3318 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14272 Z= 0.137 Angle : 0.570 15.304 19316 Z= 0.288 Chirality : 0.038 0.161 2220 Planarity : 0.003 0.021 2344 Dihedral : 5.604 55.155 1932 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.40 % Allowed : 14.31 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1660 helix: 2.12 (0.15), residues: 1072 sheet: -0.15 (0.34), residues: 220 loop : -0.02 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 419 TYR 0.015 0.001 TYR B 442 PHE 0.038 0.001 PHE A 502 TRP 0.020 0.001 TRP A 480 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14272) covalent geometry : angle 0.57025 / 0.29 (19316) hydrogen bonds : bond 0.04399 / 2.90 ( 1013) hydrogen bonds : angle 4.00350 / 2.82 ( 3171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.540 Fit side-chains REVERT: A 50 MET cc_start: 0.6840 (ppp) cc_final: 0.6524 (ppp) REVERT: A 480 TRP cc_start: 0.8016 (t60) cc_final: 0.7611 (t60) REVERT: A 491 ILE cc_start: 0.7790 (mt) cc_final: 0.7567 (mt) REVERT: B 365 MET cc_start: 0.8432 (ttt) cc_final: 0.8073 (ttp) REVERT: B 480 TRP cc_start: 0.7994 (t60) cc_final: 0.7559 (t60) REVERT: B 496 TYR cc_start: 0.8323 (t80) cc_final: 0.8084 (t80) REVERT: C 363 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7991 (tt) REVERT: C 444 GLU cc_start: 0.8064 (mp0) cc_final: 0.7796 (mp0) REVERT: C 477 ILE cc_start: 0.7799 (mm) cc_final: 0.7151 (tp) REVERT: C 481 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8306 (mp) REVERT: D 363 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7937 (tt) REVERT: D 444 GLU cc_start: 0.8027 (mp0) cc_final: 0.7767 (mp0) REVERT: D 477 ILE cc_start: 0.7773 (mm) cc_final: 0.7093 (tp) REVERT: D 481 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8280 (mp) outliers start: 37 outliers final: 27 residues processed: 217 average time/residue: 0.1034 time to fit residues: 34.7338 Evaluate side-chains 220 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [89, 167, 19, 34, 60, 121, 56, 110, 24, 85, 79] chunk 89 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.202616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137395 restraints weight = 15275.031| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.28 r_work: 0.3276 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14272 Z= 0.190 Angle : 0.609 15.450 19316 Z= 0.313 Chirality : 0.040 0.165 2220 Planarity : 0.003 0.022 2344 Dihedral : 5.835 56.708 1932 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.14 % Allowed : 14.44 % Favored : 83.42 % 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 (0.20), residues: 1660 helix: 2.01 (0.15), residues: 1072 sheet: -0.18 (0.34), residues: 220 loop : -0.07 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 419 TYR 0.017 0.002 TYR D 496 PHE 0.036 0.002 PHE A 490 TRP 0.018 0.002 TRP B 480 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (14272) covalent geometry : angle 0.60906 / 0.31 (19316) hydrogen bonds : bond 0.04743 / 3.13 ( 1013) hydrogen bonds : angle 4.16196 / 2.93 ( 3171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.601 Fit side-chains REVERT: A 50 MET cc_start: 0.6859 (ppp) cc_final: 0.6530 (ppp) REVERT: B 496 TYR cc_start: 0.8445 (t80) cc_final: 0.8189 (t80) REVERT: C 363 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8021 (tt) REVERT: C 444 GLU cc_start: 0.7839 (mp0) cc_final: 0.7590 (mp0) REVERT: C 477 ILE cc_start: 0.7885 (mm) cc_final: 0.7297 (tp) REVERT: C 481 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8256 (mp) REVERT: D 363 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8002 (tt) REVERT: D 444 GLU cc_start: 0.7819 (mp0) cc_final: 0.7568 (mp0) REVERT: D 481 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8378 (mp) outliers start: 33 outliers final: 28 residues processed: 213 average time/residue: 0.1008 time to fit residues: 33.1899 Evaluate side-chains 222 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [95, 5, 127, 32, 149, 12, 51, 87, 132, 110, 58] chunk 95 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.204951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139688 restraints weight = 15243.298| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.18 r_work: 0.3379 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14272 Z= 0.143 Angle : 0.585 15.731 19316 Z= 0.296 Chirality : 0.038 0.163 2220 Planarity : 0.003 0.022 2344 Dihedral : 5.625 55.451 1932 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.40 % Allowed : 14.25 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1660 helix: 2.08 (0.15), residues: 1072 sheet: -0.23 (0.34), residues: 220 loop : -0.06 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 419 TYR 0.017 0.001 TYR B 442 PHE 0.037 0.001 PHE C 502 TRP 0.018 0.001 TRP A 480 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14272) covalent geometry : angle 0.58498 / 0.30 (19316) hydrogen bonds : bond 0.04453 / 2.94 ( 1013) hydrogen bonds : angle 4.05714 / 2.85 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.43 seconds wall clock time: 58 minutes 19.43 seconds (3499.43 seconds total)