Starting phenix.real_space_refine on Thu Jul 2 18:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8c_15229/07_2026/8a8c_15229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8c_15229/07_2026/8a8c_15229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a8c_15229/07_2026/8a8c_15229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8c_15229/07_2026/8a8c_15229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a8c_15229/07_2026/8a8c_15229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8c_15229/07_2026/8a8c_15229.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 2 5.49 5 S 35 5.16 5 C 6023 2.51 5 N 1606 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9544 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5427 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 661} Chain: "B" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3981 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 4 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 136 Unusual residues: {'LU9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.20 Number of scatterers: 9544 At special positions: 0 Unit cell: (65.32, 76.68, 146.97, 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 35 16.00 P 2 15.00 O 1878 8.00 N 1606 7.00 C 6023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 692 " - pdb=" SG CYS A 698 " distance=2.03 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: 0.86 Conformation dependent library (CDL) restraints added in 337.6 milliseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 16 sheets defined 7.3% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.860A pdb=" N THR A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.903A pdb=" N GLY B 295 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 587 through 591 removed outlier: 3.730A pdb=" N VAL B 591 " --> pdb=" O PRO B 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.524A pdb=" N ILE A 91 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.561A pdb=" N TYR A 340 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 317 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA A 342 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 307 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.815A pdb=" N TYR A 345 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 386 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 373 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TRP A 478 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLY A 563 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 549 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU A 561 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 551 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A 559 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU A 564 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 643 Processing sheet with id=AA7, first strand: chain 'A' and resid 689 through 692 removed outlier: 7.017A pdb=" N PHE A 699 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 325 through 327 removed outlier: 4.844A pdb=" N VAL B 82 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG B 94 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASN B 380 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN B 420 " --> pdb=" O CYS B 379 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 381 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS B 418 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE B 45 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 317 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 47 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AB1, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.413A pdb=" N TYR B 601 " --> pdb=" O PHE B 559 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 615 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS B 481 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER B 617 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER B 479 " --> pdb=" O SER B 617 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 258 removed outlier: 4.174A pdb=" N ALA B 253 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE B 272 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 255 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 270 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 257 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B 268 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 275 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 158 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.408A pdb=" N ILE B 202 " --> pdb=" O GLY B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.565A pdb=" N TYR B 300 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AB6, first strand: chain 'B' and resid 459 through 468 removed outlier: 6.711A pdb=" N GLY B 462 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG B 638 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 632 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA B 496 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 471 through 474 424 hydrogen bonds defined for protein. 1161 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: 1.54 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1583 1.31 - 1.43: 2795 1.43 - 1.56: 5308 1.56 - 1.69: 32 1.69 - 1.81: 59 Bond restraints: 9777 Sorted by residual: bond pdb=" C81 LU9 A 801 " pdb=" O81 LU9 A 801 " ideal model delta sigma weight residual 1.204 1.395 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C01 LU9 A 801 " pdb=" O03 LU9 A 801 " ideal model delta sigma weight residual 1.243 1.414 -0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" C71 LU9 A 801 " pdb=" O71 LU9 A 801 " ideal model delta sigma weight residual 1.203 1.373 -0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" NB2 LU9 A 801 " pdb=" C51 LU9 A 801 " ideal model delta sigma weight residual 1.347 1.512 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" C11 LU9 A 801 " pdb=" NA2 LU9 A 801 " ideal model delta sigma weight residual 1.344 1.507 -0.163 2.00e-02 2.50e+03 6.62e+01 ... (remaining 9772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 13217 4.35 - 8.70: 49 8.70 - 13.06: 4 13.06 - 17.41: 5 17.41 - 21.76: 1 Bond angle restraints: 13276 Sorted by residual: angle pdb=" C19 LU9 A 801 " pdb="C110 LU9 A 801 " pdb="C111 LU9 A 801 " ideal model delta sigma weight residual 114.73 136.49 -21.76 3.00e+00 1.11e-01 5.26e+01 angle pdb=" C82 LU9 A 801 " pdb=" C81 LU9 A 801 " pdb=" O81 LU9 A 801 " ideal model delta sigma weight residual 125.22 109.24 15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O02 LU9 A 801 " pdb=" C01 LU9 A 801 " pdb=" O03 LU9 A 801 " ideal model delta sigma weight residual 127.57 112.39 15.18 3.00e+00 1.11e-01 2.56e+01 angle pdb=" OB3 LU9 A 801 " pdb=" C71 LU9 A 801 " pdb=" O71 LU9 A 801 " ideal model delta sigma weight residual 124.63 109.68 14.95 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C72 LU9 A 801 " pdb=" C71 LU9 A 801 " pdb=" O71 LU9 A 801 " ideal model delta sigma weight residual 123.61 108.95 14.66 3.00e+00 1.11e-01 2.39e+01 ... (remaining 13271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5035 17.90 - 35.80: 620 35.80 - 53.70: 130 53.70 - 71.61: 27 71.61 - 89.51: 16 Dihedral angle restraints: 5828 sinusoidal: 2356 harmonic: 3472 Sorted by residual: dihedral pdb=" CA ALA B 186 " pdb=" C ALA B 186 " pdb=" N TRP B 187 " pdb=" CA TRP B 187 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER A 326 " pdb=" C SER A 326 " pdb=" N LYS A 327 " pdb=" CA LYS A 327 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR A 325 " pdb=" C TYR A 325 " pdb=" N SER A 326 " pdb=" CA SER A 326 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1166 0.056 - 0.113: 220 0.113 - 0.169: 28 0.169 - 0.226: 3 0.226 - 0.282: 1 Chirality restraints: 1418 Sorted by residual: chirality pdb=" C2 LU9 A 801 " pdb=" C3 LU9 A 801 " pdb=" O05 LU9 A 801 " pdb=" O6 LU9 A 801 " both_signs ideal model delta sigma weight residual False -2.31 -2.60 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA5 LU9 A 801 " pdb=" CA4 LU9 A 801 " pdb=" CA6 LU9 A 801 " pdb=" OA5 LU9 A 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.51 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB5 LU9 A 801 " pdb=" CB4 LU9 A 801 " pdb=" CB6 LU9 A 801 " pdb=" OB5 LU9 A 801 " both_signs ideal model delta sigma weight residual False -2.44 -2.63 0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 1415 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C81 LU9 A 801 " -0.362 2.00e-02 2.50e+03 2.09e-01 4.36e+02 pdb=" C82 LU9 A 801 " 0.112 2.00e-02 2.50e+03 pdb=" O73 LU9 A 801 " 0.124 2.00e-02 2.50e+03 pdb=" O81 LU9 A 801 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" OB3 LU9 A 801 " 0.124 2.00e-02 2.50e+03 2.08e-01 4.33e+02 pdb=" C71 LU9 A 801 " -0.360 2.00e-02 2.50e+03 pdb=" C72 LU9 A 801 " 0.109 2.00e-02 2.50e+03 pdb=" O71 LU9 A 801 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 LU9 A 801 " -0.351 2.00e-02 2.50e+03 2.03e-01 4.11e+02 pdb=" C02 LU9 A 801 " 0.108 2.00e-02 2.50e+03 pdb=" O02 LU9 A 801 " 0.122 2.00e-02 2.50e+03 pdb=" O03 LU9 A 801 " 0.122 2.00e-02 2.50e+03 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 824 2.74 - 3.28: 9442 3.28 - 3.82: 16970 3.82 - 4.36: 21398 4.36 - 4.90: 38015 Nonbonded interactions: 86649 Sorted by model distance: nonbonded pdb=" O ASN B 238 " pdb=" OG1 THR B 241 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 234 " pdb=" OE1 GLN A 236 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 243 " pdb=" OE1 GLU A 268 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 182 " pdb=" N SER A 183 " model vdw 2.238 3.120 nonbonded pdb=" NE2 GLN B 158 " pdb=" O ASP B 276 " model vdw 2.238 3.120 ... (remaining 86644 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.220 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: 9.480 Find NCS groups from input model: 0.040 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 : 0.008 0.191 9779 Z= 0.370 Angle : 0.755 21.759 13280 Z= 0.337 Chirality : 0.046 0.282 1418 Planarity : 0.010 0.209 1734 Dihedral : 16.616 89.508 3638 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.94 % Favored : 93.89 % Rotamer: Outliers : 0.80 % Allowed : 25.50 % Favored : 73.70 % 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: -1.68 (0.24), residues: 1212 helix: -2.24 (0.59), residues: 68 sheet: -1.03 (0.23), residues: 545 loop : -0.91 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 532 TYR 0.026 0.001 TYR B 109 PHE 0.013 0.001 PHE A 115 TRP 0.010 0.001 TRP B 187 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.37 ( 9777) covalent geometry : angle 0.75524 / 0.34 (13276) SS BOND : bond 0.00308 / 0.16 ( 2) SS BOND : angle 0.68091 / 0.36 ( 4) hydrogen bonds : bond 0.23895 / 17.02 ( 420) hydrogen bonds : angle 11.04365 / 7.68 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.334 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.0573 time to fit residues: 9.5370 Evaluate side-chains 98 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 112 GLN A 114 ASN A 385 ASN A 427 ASN B 125 GLN B 294 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122034 restraints weight = 10843.691| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.41 r_work: 0.3311 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9779 Z= 0.162 Angle : 0.577 10.195 13280 Z= 0.301 Chirality : 0.046 0.148 1418 Planarity : 0.005 0.079 1734 Dihedral : 5.978 67.689 1557 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.70 % Favored : 95.13 % Rotamer: Outliers : 3.50 % Allowed : 23.00 % Favored : 73.50 % 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: -1.65 (0.24), residues: 1212 helix: -2.00 (0.60), residues: 70 sheet: -0.99 (0.24), residues: 503 loop : -0.96 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.017 0.001 TYR A 325 PHE 0.013 0.001 PHE B 256 TRP 0.012 0.001 TRP B 187 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 9777) covalent geometry : angle 0.57712 / 0.30 (13276) SS BOND : bond 0.00541 / 0.28 ( 2) SS BOND : angle 1.00959 / 0.56 ( 4) hydrogen bonds : bond 0.04664 / 3.29 ( 420) hydrogen bonds : angle 7.64831 / 5.32 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.344 Fit side-chains REVERT: A 637 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7508 (mtm110) REVERT: B 401 THR cc_start: 0.8646 (m) cc_final: 0.8329 (p) outliers start: 35 outliers final: 18 residues processed: 141 average time/residue: 0.0638 time to fit residues: 13.9006 Evaluate side-chains 120 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 117 optimal weight: 0.1980 chunk 2 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN B 125 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125091 restraints weight = 10720.112| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.59 r_work: 0.3385 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9779 Z= 0.138 Angle : 0.541 9.863 13280 Z= 0.280 Chirality : 0.045 0.153 1418 Planarity : 0.004 0.065 1734 Dihedral : 5.591 69.155 1553 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.46 % Rotamer: Outliers : 3.80 % Allowed : 23.00 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1212 helix: -1.90 (0.62), residues: 70 sheet: -1.00 (0.23), residues: 505 loop : -0.90 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 375 TYR 0.018 0.001 TYR A 325 PHE 0.011 0.001 PHE B 256 TRP 0.012 0.001 TRP B 187 HIS 0.003 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9777) covalent geometry : angle 0.54094 / 0.28 (13276) SS BOND : bond 0.00544 / 0.28 ( 2) SS BOND : angle 1.16501 / 0.65 ( 4) hydrogen bonds : bond 0.03608 / 2.54 ( 420) hydrogen bonds : angle 7.02467 / 4.90 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.235 Fit side-chains REVERT: A 399 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8493 (mt) REVERT: B 246 GLN cc_start: 0.8172 (mt0) cc_final: 0.7958 (mt0) REVERT: B 401 THR cc_start: 0.8558 (m) cc_final: 0.8169 (p) REVERT: B 509 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7461 (pp) REVERT: B 544 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8384 (mtmm) outliers start: 38 outliers final: 25 residues processed: 143 average time/residue: 0.0586 time to fit residues: 13.1630 Evaluate side-chains 130 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 117 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 ASN B 125 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123148 restraints weight = 10783.150| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.59 r_work: 0.3363 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9779 Z= 0.182 Angle : 0.559 10.627 13280 Z= 0.288 Chirality : 0.046 0.143 1418 Planarity : 0.004 0.060 1734 Dihedral : 5.606 69.138 1553 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 5.40 % Allowed : 21.90 % Favored : 72.70 % 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: -1.64 (0.24), residues: 1212 helix: -1.92 (0.62), residues: 70 sheet: -1.04 (0.23), residues: 498 loop : -0.91 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 375 TYR 0.021 0.001 TYR B 109 PHE 0.011 0.001 PHE B 256 TRP 0.012 0.001 TRP B 187 HIS 0.005 0.001 HIS A 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 9777) covalent geometry : angle 0.55881 / 0.29 (13276) SS BOND : bond 0.00554 / 0.28 ( 2) SS BOND : angle 1.15969 / 0.64 ( 4) hydrogen bonds : bond 0.03417 / 2.42 ( 420) hydrogen bonds : angle 6.84814 / 4.79 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 0.295 Fit side-chains REVERT: A 399 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 246 GLN cc_start: 0.8333 (mt0) cc_final: 0.8110 (mt0) REVERT: B 401 THR cc_start: 0.8601 (m) cc_final: 0.8215 (p) REVERT: B 509 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7561 (pp) REVERT: B 544 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8325 (mtmm) outliers start: 54 outliers final: 39 residues processed: 152 average time/residue: 0.0604 time to fit residues: 14.4949 Evaluate side-chains 142 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 639 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 100 optimal weight: 0.0010 chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 4 optimal weight: 0.0030 chunk 109 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.1472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN A 385 ASN B 125 GLN B 149 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128420 restraints weight = 10839.795| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.42 r_work: 0.3398 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9779 Z= 0.103 Angle : 0.523 8.439 13280 Z= 0.266 Chirality : 0.044 0.143 1418 Planarity : 0.004 0.059 1734 Dihedral : 5.238 68.936 1553 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 4.00 % Allowed : 24.00 % Favored : 72.00 % 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: -1.49 (0.24), residues: 1212 helix: -1.87 (0.64), residues: 70 sheet: -0.95 (0.23), residues: 504 loop : -0.79 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 375 TYR 0.023 0.001 TYR B 109 PHE 0.009 0.001 PHE B 256 TRP 0.012 0.001 TRP B 187 HIS 0.003 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9777) covalent geometry : angle 0.52244 / 0.27 (13276) SS BOND : bond 0.00500 / 0.26 ( 2) SS BOND : angle 1.29611 / 0.74 ( 4) hydrogen bonds : bond 0.02814 / 1.93 ( 420) hydrogen bonds : angle 6.36229 / 4.45 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.240 Fit side-chains REVERT: A 125 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8046 (mtp) REVERT: A 399 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8435 (mt) REVERT: B 401 THR cc_start: 0.8494 (m) cc_final: 0.8288 (p) REVERT: B 509 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7555 (pp) REVERT: B 544 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8275 (mtmm) outliers start: 40 outliers final: 24 residues processed: 154 average time/residue: 0.0622 time to fit residues: 14.6116 Evaluate side-chains 130 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 639 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122608 restraints weight = 11000.565| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.43 r_work: 0.3322 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9779 Z= 0.173 Angle : 0.563 10.175 13280 Z= 0.285 Chirality : 0.046 0.189 1418 Planarity : 0.004 0.058 1734 Dihedral : 5.447 68.120 1553 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.80 % Rotamer: Outliers : 4.20 % Allowed : 24.10 % Favored : 71.70 % 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: -1.53 (0.24), residues: 1212 helix: -1.93 (0.62), residues: 70 sheet: -0.95 (0.23), residues: 516 loop : -0.83 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 301 TYR 0.026 0.001 TYR B 109 PHE 0.011 0.001 PHE A 115 TRP 0.011 0.001 TRP B 187 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 9777) covalent geometry : angle 0.56312 / 0.28 (13276) SS BOND : bond 0.00539 / 0.28 ( 2) SS BOND : angle 1.25305 / 0.69 ( 4) hydrogen bonds : bond 0.03103 / 2.19 ( 420) hydrogen bonds : angle 6.41536 / 4.48 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.318 Fit side-chains REVERT: A 125 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: A 399 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 116 ILE cc_start: 0.8927 (mt) cc_final: 0.8725 (mp) REVERT: B 401 THR cc_start: 0.8598 (m) cc_final: 0.8296 (p) REVERT: B 509 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7631 (pp) REVERT: B 544 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (mtmm) outliers start: 42 outliers final: 34 residues processed: 141 average time/residue: 0.0534 time to fit residues: 12.2109 Evaluate side-chains 143 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 639 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120032 restraints weight = 10964.845| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.35 r_work: 0.3295 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9779 Z= 0.237 Angle : 0.597 10.808 13280 Z= 0.304 Chirality : 0.047 0.180 1418 Planarity : 0.004 0.061 1734 Dihedral : 5.741 68.062 1553 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 5.10 % Allowed : 23.10 % Favored : 71.80 % 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: -1.65 (0.24), residues: 1212 helix: -1.99 (0.61), residues: 70 sheet: -1.05 (0.23), residues: 489 loop : -0.92 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 274 TYR 0.024 0.002 TYR B 109 PHE 0.012 0.001 PHE B 256 TRP 0.010 0.001 TRP B 187 HIS 0.005 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 ( 9777) covalent geometry : angle 0.59721 / 0.30 (13276) SS BOND : bond 0.00612 / 0.31 ( 2) SS BOND : angle 1.15538 / 0.63 ( 4) hydrogen bonds : bond 0.03285 / 2.32 ( 420) hydrogen bonds : angle 6.65725 / 4.66 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 97 time to evaluate : 0.323 Fit side-chains REVERT: A 125 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8028 (mtp) REVERT: A 399 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8660 (mt) REVERT: B 401 THR cc_start: 0.8648 (m) cc_final: 0.8366 (p) REVERT: B 509 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7649 (pp) REVERT: B 536 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8453 (mm) outliers start: 51 outliers final: 39 residues processed: 137 average time/residue: 0.0589 time to fit residues: 12.9724 Evaluate side-chains 138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 639 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 117 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122668 restraints weight = 10842.046| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.31 r_work: 0.3314 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9779 Z= 0.199 Angle : 0.581 10.397 13280 Z= 0.296 Chirality : 0.046 0.163 1418 Planarity : 0.004 0.061 1734 Dihedral : 5.738 68.608 1553 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 5.00 % Allowed : 23.60 % Favored : 71.40 % 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: -1.71 (0.24), residues: 1212 helix: -1.95 (0.61), residues: 70 sheet: -1.14 (0.23), residues: 509 loop : -0.91 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.024 0.002 TYR B 109 PHE 0.013 0.001 PHE B 256 TRP 0.009 0.001 TRP B 187 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 9777) covalent geometry : angle 0.58097 / 0.30 (13276) SS BOND : bond 0.00590 / 0.30 ( 2) SS BOND : angle 1.28018 / 0.71 ( 4) hydrogen bonds : bond 0.03146 / 2.18 ( 420) hydrogen bonds : angle 6.63723 / 4.65 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 0.339 Fit side-chains REVERT: A 125 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8016 (mtp) REVERT: A 399 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8676 (mt) REVERT: B 401 THR cc_start: 0.8655 (m) cc_final: 0.8419 (p) REVERT: B 509 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 536 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8432 (mm) REVERT: B 544 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8098 (mtmm) REVERT: B 606 ASP cc_start: 0.7560 (m-30) cc_final: 0.7349 (m-30) REVERT: B 637 GLN cc_start: 0.8526 (tt0) cc_final: 0.8145 (tp40) outliers start: 50 outliers final: 42 residues processed: 138 average time/residue: 0.0585 time to fit residues: 13.0544 Evaluate side-chains 145 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123962 restraints weight = 10913.788| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.37 r_work: 0.3325 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9779 Z= 0.152 Angle : 0.557 9.740 13280 Z= 0.284 Chirality : 0.045 0.163 1418 Planarity : 0.004 0.061 1734 Dihedral : 5.562 69.029 1553 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 4.50 % Allowed : 24.20 % Favored : 71.30 % 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: -1.70 (0.24), residues: 1212 helix: -1.84 (0.63), residues: 70 sheet: -1.11 (0.22), residues: 516 loop : -0.94 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.025 0.001 TYR B 109 PHE 0.012 0.001 PHE B 256 TRP 0.008 0.001 TRP B 187 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 9777) covalent geometry : angle 0.55644 / 0.28 (13276) SS BOND : bond 0.00556 / 0.29 ( 2) SS BOND : angle 1.31276 / 0.73 ( 4) hydrogen bonds : bond 0.02943 / 2.03 ( 420) hydrogen bonds : angle 6.49124 / 4.55 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.372 Fit side-chains REVERT: A 125 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7992 (mtp) REVERT: A 399 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8659 (mt) REVERT: B 509 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7659 (pp) REVERT: B 536 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8374 (mm) REVERT: B 637 GLN cc_start: 0.8528 (tt0) cc_final: 0.8246 (tp40) outliers start: 45 outliers final: 36 residues processed: 136 average time/residue: 0.0617 time to fit residues: 13.8102 Evaluate side-chains 136 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 639 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120816 restraints weight = 10927.418| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.40 r_work: 0.3301 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9779 Z= 0.185 Angle : 0.575 10.287 13280 Z= 0.294 Chirality : 0.046 0.174 1418 Planarity : 0.004 0.061 1734 Dihedral : 5.647 69.327 1553 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 4.20 % Allowed : 24.70 % Favored : 71.10 % 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: -1.75 (0.24), residues: 1212 helix: -1.89 (0.62), residues: 70 sheet: -1.17 (0.22), residues: 516 loop : -0.93 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.027 0.001 TYR B 109 PHE 0.013 0.001 PHE A 115 TRP 0.008 0.001 TRP B 187 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 9777) covalent geometry : angle 0.57435 / 0.29 (13276) SS BOND : bond 0.00553 / 0.28 ( 2) SS BOND : angle 1.24756 / 0.69 ( 4) hydrogen bonds : bond 0.03038 / 2.11 ( 420) hydrogen bonds : angle 6.54493 / 4.58 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.350 Fit side-chains REVERT: A 35 THR cc_start: 0.8762 (p) cc_final: 0.8493 (t) REVERT: A 125 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8002 (mtp) REVERT: A 399 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8698 (mt) REVERT: B 509 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7657 (pp) REVERT: B 536 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8401 (mm) REVERT: B 544 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8126 (mtmm) REVERT: B 637 GLN cc_start: 0.8562 (tt0) cc_final: 0.8306 (tp40) outliers start: 42 outliers final: 36 residues processed: 132 average time/residue: 0.0640 time to fit residues: 13.7706 Evaluate side-chains 141 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 639 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121725 restraints weight = 10837.864| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.35 r_work: 0.3314 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9779 Z= 0.190 Angle : 0.582 10.317 13280 Z= 0.298 Chirality : 0.047 0.174 1418 Planarity : 0.004 0.061 1734 Dihedral : 5.691 71.473 1553 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 4.70 % Allowed : 24.30 % Favored : 71.00 % 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: -1.77 (0.24), residues: 1212 helix: -1.91 (0.61), residues: 70 sheet: -1.19 (0.22), residues: 516 loop : -0.94 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.027 0.001 TYR B 109 PHE 0.013 0.001 PHE B 256 TRP 0.008 0.001 TRP B 187 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 9777) covalent geometry : angle 0.58183 / 0.30 (13276) SS BOND : bond 0.00554 / 0.28 ( 2) SS BOND : angle 1.21721 / 0.67 ( 4) hydrogen bonds : bond 0.03056 / 2.12 ( 420) hydrogen bonds : angle 6.57184 / 4.60 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.87 seconds wall clock time: 35 minutes 49.50 seconds (2149.50 seconds total)