Starting phenix.real_space_refine on Fri Jul 3 06:35:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9waa_65810/07_2026/9waa_65810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9waa_65810/07_2026/9waa_65810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9waa_65810/07_2026/9waa_65810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9waa_65810/07_2026/9waa_65810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9waa_65810/07_2026/9waa_65810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9waa_65810/07_2026/9waa_65810.map" } resolution = 4.17 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= 0.003 sd= 0.032 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 147 5.49 5 S 18 5.16 5 C 7313 2.51 5 N 2178 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 12359 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9201 Classifications: {'peptide': 1129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1098} Chain breaks: 2 Chain: "B" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 761 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2111 Classifications: {'RNA': 99} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 39} Link IDs: {'rna2p': 11, 'rna3p': 87} Time building chain proxies: 2.84, per 1000 atoms: 0.23 Number of scatterers: 12359 At special positions: 0 Unit cell: (136.398, 115.992, 111.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 147 15.00 O 2703 8.00 N 2178 7.00 C 7313 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: 0.97 Conformation dependent library (CDL) restraints added in 476.8 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 55.4% alpha, 8.0% beta 59 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 removed outlier: 4.695A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.589A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.504A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.604A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.874A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 removed outlier: 4.600A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 305 removed outlier: 3.585A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.696A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.329A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 495 removed outlier: 4.182A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.859A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.481A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.512A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.957A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.433A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.563A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1311 removed outlier: 3.704A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.923A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 4.208A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.653A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.585A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509 removed outlier: 4.812A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.588A pdb=" N TYR A 529 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.728A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326 434 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2866 1.33 - 1.45: 3252 1.45 - 1.57: 6458 1.57 - 1.69: 294 1.69 - 1.81: 34 Bond restraints: 12904 Sorted by residual: bond pdb=" C3' DG B 11 " pdb=" C2' DG B 11 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 bond pdb=" C3' DC C 8 " pdb=" C2' DC C 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DC B 16 " pdb=" C2' DC B 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.75e+00 bond pdb=" C3' DT B 33 " pdb=" C2' DT B 33 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.73e+00 bond pdb=" C3' DA B 8 " pdb=" C2' DA B 8 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.00e+00 ... (remaining 12899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 17963 2.47 - 4.94: 117 4.94 - 7.40: 0 7.40 - 9.87: 0 9.87 - 12.34: 1 Bond angle restraints: 18081 Sorted by residual: angle pdb=" O4' DG B 32 " pdb=" C4' DG B 32 " pdb=" C3' DG B 32 " ideal model delta sigma weight residual 106.00 102.22 3.78 6.00e-01 2.78e+00 3.97e+01 angle pdb=" O4' DA B 22 " pdb=" C4' DA B 22 " pdb=" C3' DA B 22 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" O4' DG B 28 " pdb=" C4' DG B 28 " pdb=" C3' DG B 28 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4' DT B 17 " pdb=" C4' DT B 17 " pdb=" C3' DT B 17 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 2.00e+01 ... (remaining 18076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 7367 30.04 - 60.09: 353 60.09 - 90.13: 78 90.13 - 120.18: 1 120.18 - 150.22: 1 Dihedral angle restraints: 7800 sinusoidal: 4485 harmonic: 3315 Sorted by residual: dihedral pdb=" C4' DG B 7 " pdb=" C3' DG B 7 " pdb=" O3' DG B 7 " pdb=" P DA B 8 " ideal model delta sinusoidal sigma weight residual 220.00 69.78 150.22 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CG ARG A1359 " pdb=" CD ARG A1359 " pdb=" NE ARG A1359 " pdb=" CZ ARG A1359 " ideal model delta sinusoidal sigma weight residual -90.00 -134.87 44.87 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" N LYS A1158 " pdb=" CA LYS A1158 " pdb=" CB LYS A1158 " pdb=" CG LYS A1158 " ideal model delta sinusoidal sigma weight residual -60.00 -116.25 56.25 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 7797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1476 0.032 - 0.064: 423 0.064 - 0.097: 128 0.097 - 0.129: 58 0.129 - 0.161: 3 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CA ILE A 305 " pdb=" N ILE A 305 " pdb=" C ILE A 305 " pdb=" CB ILE A 305 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" C1' A D 36 " pdb=" O4' A D 36 " pdb=" C2' A D 36 " pdb=" N9 A D 36 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2085 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 653 " 0.173 9.50e-02 1.11e+02 7.76e-02 3.70e+00 pdb=" NE ARG A 653 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 653 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 653 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 653 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 44 " 0.024 2.00e-02 2.50e+03 1.08e-02 3.18e+00 pdb=" N9 A D 44 " -0.025 2.00e-02 2.50e+03 pdb=" C8 A D 44 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A D 44 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A D 44 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A D 44 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 44 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A D 44 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 44 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 36 " 0.020 2.00e-02 2.50e+03 9.26e-03 2.36e+00 pdb=" N9 A D 36 " -0.023 2.00e-02 2.50e+03 pdb=" C8 A D 36 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A D 36 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D 36 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 36 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A D 36 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A D 36 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 36 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 36 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 36 " -0.002 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 990 2.74 - 3.46: 17070 3.46 - 4.18: 31229 4.18 - 4.90: 49602 Nonbonded interactions: 98896 Sorted by model distance: nonbonded pdb=" NZ LYS A 742 " pdb=" OP1 C D 69 " model vdw 1.296 3.120 nonbonded pdb=" NZ LYS A1340 " pdb=" OP2 DA B 8 " model vdw 1.297 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" N4 C D 20 " model vdw 1.352 3.200 nonbonded pdb=" CA GLY A 582 " pdb=" OP1 DC B 34 " model vdw 1.375 3.440 nonbonded pdb=" N GLY A 582 " pdb=" OP1 DC B 34 " model vdw 1.920 3.120 ... (remaining 98891 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 0.033 12904 Z= 0.260 Angle : 0.556 12.340 18081 Z= 0.440 Chirality : 0.037 0.161 2088 Planarity : 0.004 0.078 1762 Dihedral : 16.334 150.220 5654 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 1.55 (0.26), residues: 1123 helix: 1.87 (0.23), residues: 577 sheet: 1.65 (0.64), residues: 71 loop : -0.08 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.010 0.001 TYR A1356 PHE 0.009 0.001 PHE A 432 TRP 0.010 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.26 (12904) covalent geometry : angle 0.55627 / 0.44 (18081) hydrogen bonds : bond 0.14587 / 9.55 ( 584) hydrogen bonds : angle 5.47416 / 3.90 ( 1559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 THR cc_start: 0.7978 (p) cc_final: 0.7563 (t) REVERT: A 517 TYR cc_start: 0.8645 (m-80) cc_final: 0.8406 (m-80) REVERT: A 667 ILE cc_start: 0.9265 (mt) cc_final: 0.8732 (mt) REVERT: A 668 ASN cc_start: 0.9382 (t0) cc_final: 0.9161 (m110) REVERT: A 1135 ASP cc_start: 0.7374 (t0) cc_final: 0.7017 (t70) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1533 time to fit residues: 41.6879 Evaluate side-chains 115 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 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 = 0.3378 r_free = 0.3378 target = 0.051059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.038042 restraints weight = 106807.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039009 restraints weight = 66486.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.039668 restraints weight = 48530.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.040126 restraints weight = 39384.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.040450 restraints weight = 34113.684| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12904 Z= 0.217 Angle : 0.645 8.373 18081 Z= 0.364 Chirality : 0.042 0.203 2088 Planarity : 0.005 0.061 1762 Dihedral : 18.882 155.778 3276 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.12 (0.24), residues: 1123 helix: 1.54 (0.21), residues: 582 sheet: 1.03 (0.54), residues: 90 loop : -0.31 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 71 TYR 0.018 0.002 TYR A1201 PHE 0.016 0.002 PHE A1276 TRP 0.014 0.002 TRP A 659 HIS 0.006 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.22 (12904) covalent geometry : angle 0.64453 / 0.36 (18081) hydrogen bonds : bond 0.05899 / 4.03 ( 584) hydrogen bonds : angle 4.69194 / 3.36 ( 1559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9518 (pm20) cc_final: 0.9228 (pm20) REVERT: A 75 ARG cc_start: 0.9768 (ttp-170) cc_final: 0.9488 (mmt-90) REVERT: A 415 HIS cc_start: 0.9433 (m90) cc_final: 0.9013 (m90) REVERT: A 517 TYR cc_start: 0.9018 (m-80) cc_final: 0.8667 (m-80) REVERT: A 518 PHE cc_start: 0.9649 (t80) cc_final: 0.9202 (t80) REVERT: A 667 ILE cc_start: 0.9463 (mt) cc_final: 0.8724 (mt) REVERT: A 668 ASN cc_start: 0.9580 (t0) cc_final: 0.9272 (m-40) REVERT: A 724 ILE cc_start: 0.9276 (mt) cc_final: 0.8947 (tt) REVERT: A 751 MET cc_start: 0.9446 (mmp) cc_final: 0.8952 (mmm) REVERT: A 926 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8966 (mt0) REVERT: A 943 TYR cc_start: 0.9439 (p90) cc_final: 0.9235 (p90) REVERT: A 1089 MET cc_start: 0.8705 (tpt) cc_final: 0.7910 (tpp) REVERT: A 1126 TRP cc_start: 0.9114 (m-10) cc_final: 0.8799 (m-10) REVERT: A 1170 GLU cc_start: 0.9470 (tp30) cc_final: 0.9228 (tm-30) REVERT: A 1171 ARG cc_start: 0.9702 (ttt180) cc_final: 0.9400 (ttm170) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1386 time to fit residues: 23.9223 Evaluate side-chains 91 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 115 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 5.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.068721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.058062 restraints weight = 129243.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.059373 restraints weight = 66190.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.060103 restraints weight = 41676.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.060613 restraints weight = 31459.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.060870 restraints weight = 25967.034| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12904 Z= 0.185 Angle : 0.581 8.521 18081 Z= 0.335 Chirality : 0.041 0.292 2088 Planarity : 0.004 0.057 1762 Dihedral : 19.045 155.063 3276 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.17 (0.24), residues: 1123 helix: 1.65 (0.21), residues: 570 sheet: 1.53 (0.63), residues: 59 loop : -0.32 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1303 TYR 0.014 0.002 TYR A1141 PHE 0.017 0.002 PHE A 626 TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (12904) covalent geometry : angle 0.58090 / 0.34 (18081) hydrogen bonds : bond 0.04899 / 3.32 ( 584) hydrogen bonds : angle 4.46237 / 3.20 ( 1559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9533 (pm20) cc_final: 0.9225 (pm20) REVERT: A 415 HIS cc_start: 0.9429 (m90) cc_final: 0.8894 (m90) REVERT: A 517 TYR cc_start: 0.9039 (m-80) cc_final: 0.8708 (m-80) REVERT: A 518 PHE cc_start: 0.9601 (t80) cc_final: 0.9087 (t80) REVERT: A 534 MET cc_start: 0.5649 (ttt) cc_final: 0.5168 (ttt) REVERT: A 668 ASN cc_start: 0.9543 (t0) cc_final: 0.9203 (m-40) REVERT: A 724 ILE cc_start: 0.9254 (mt) cc_final: 0.8888 (tt) REVERT: A 751 MET cc_start: 0.9390 (mmp) cc_final: 0.8916 (mmm) REVERT: A 926 GLN cc_start: 0.9350 (mm-40) cc_final: 0.8998 (mt0) REVERT: A 943 TYR cc_start: 0.9397 (p90) cc_final: 0.9086 (p90) REVERT: A 1089 MET cc_start: 0.8852 (tpt) cc_final: 0.7807 (tpp) REVERT: A 1170 GLU cc_start: 0.9424 (tp30) cc_final: 0.9190 (tm-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1176 time to fit residues: 18.7524 Evaluate side-chains 82 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 10 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 115 optimal weight: 40.0000 chunk 3 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 9 optimal weight: 0.0170 overall best weight: 7.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 556 ASN ** A 723 HIS ** 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 = 0.3472 r_free = 0.3472 target = 0.065072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.054637 restraints weight = 132877.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.055861 restraints weight = 68093.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.056554 restraints weight = 43285.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.057055 restraints weight = 32909.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.057341 restraints weight = 27121.271| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12904 Z= 0.225 Angle : 0.631 12.166 18081 Z= 0.362 Chirality : 0.041 0.248 2088 Planarity : 0.005 0.094 1762 Dihedral : 19.231 156.478 3276 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1123 helix: 1.36 (0.21), residues: 582 sheet: 1.18 (0.63), residues: 59 loop : -0.32 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 75 TYR 0.016 0.002 TYR A 639 PHE 0.016 0.002 PHE A 626 TRP 0.013 0.002 TRP A 476 HIS 0.007 0.002 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.22 (12904) covalent geometry : angle 0.63114 / 0.36 (18081) hydrogen bonds : bond 0.05836 / 4.00 ( 584) hydrogen bonds : angle 4.53630 / 3.22 ( 1559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9564 (pm20) cc_final: 0.9241 (pm20) REVERT: A 415 HIS cc_start: 0.9323 (m90) cc_final: 0.8833 (m90) REVERT: A 517 TYR cc_start: 0.9096 (m-80) cc_final: 0.8700 (m-80) REVERT: A 518 PHE cc_start: 0.9627 (t80) cc_final: 0.9126 (t80) REVERT: A 534 MET cc_start: 0.5712 (ttt) cc_final: 0.5307 (ttt) REVERT: A 667 ILE cc_start: 0.9516 (mt) cc_final: 0.8759 (mt) REVERT: A 668 ASN cc_start: 0.9585 (t0) cc_final: 0.9229 (m-40) REVERT: A 724 ILE cc_start: 0.9315 (mt) cc_final: 0.8979 (tt) REVERT: A 751 MET cc_start: 0.9360 (mmp) cc_final: 0.8941 (mmm) REVERT: A 926 GLN cc_start: 0.9374 (mm-40) cc_final: 0.9055 (mt0) REVERT: A 943 TYR cc_start: 0.9375 (p90) cc_final: 0.9062 (p90) REVERT: A 1089 MET cc_start: 0.8845 (tpt) cc_final: 0.8202 (tpp) REVERT: A 1126 TRP cc_start: 0.9071 (m-10) cc_final: 0.8859 (m-10) REVERT: A 1170 GLU cc_start: 0.9440 (tp30) cc_final: 0.9075 (tp30) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1193 time to fit residues: 17.8413 Evaluate side-chains 79 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 40.0000 chunk 60 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 HIS ** 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 = 0.3518 r_free = 0.3518 target = 0.067429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.056903 restraints weight = 129538.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.058165 restraints weight = 65996.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.058955 restraints weight = 41696.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.059441 restraints weight = 30933.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.059729 restraints weight = 25429.679| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12904 Z= 0.120 Angle : 0.526 10.108 18081 Z= 0.303 Chirality : 0.039 0.226 2088 Planarity : 0.004 0.055 1762 Dihedral : 19.213 157.509 3276 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.10 % Allowed : 0.89 % Favored : 99.01 % 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: 1.08 (0.25), residues: 1123 helix: 1.55 (0.21), residues: 581 sheet: 0.45 (0.52), residues: 90 loop : -0.25 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1303 TYR 0.012 0.001 TYR A 430 PHE 0.011 0.001 PHE A 626 TRP 0.005 0.001 TRP A 476 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 (12904) covalent geometry : angle 0.52595 / 0.30 (18081) hydrogen bonds : bond 0.04042 / 2.75 ( 584) hydrogen bonds : angle 4.31667 / 3.08 ( 1559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9591 (pm20) cc_final: 0.9227 (pm20) REVERT: A 415 HIS cc_start: 0.9429 (m-70) cc_final: 0.8877 (m90) REVERT: A 517 TYR cc_start: 0.9058 (m-80) cc_final: 0.8711 (m-80) REVERT: A 518 PHE cc_start: 0.9632 (t80) cc_final: 0.9144 (t80) REVERT: A 534 MET cc_start: 0.5579 (ttt) cc_final: 0.5153 (ttt) REVERT: A 631 MET cc_start: 0.9091 (ptp) cc_final: 0.8647 (ptm) REVERT: A 648 MET cc_start: 0.8936 (mmp) cc_final: 0.8680 (mmm) REVERT: A 668 ASN cc_start: 0.9586 (t0) cc_final: 0.9215 (m110) REVERT: A 724 ILE cc_start: 0.9316 (mt) cc_final: 0.8975 (tt) REVERT: A 751 MET cc_start: 0.9253 (mmp) cc_final: 0.8826 (mmm) REVERT: A 926 GLN cc_start: 0.9369 (mm-40) cc_final: 0.9068 (mt0) REVERT: A 943 TYR cc_start: 0.9393 (p90) cc_final: 0.9079 (p90) REVERT: A 1089 MET cc_start: 0.8750 (tpt) cc_final: 0.8293 (tpp) REVERT: A 1170 GLU cc_start: 0.9425 (tp30) cc_final: 0.9015 (tp30) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1155 time to fit residues: 17.7970 Evaluate side-chains 82 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 40.0000 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 120 optimal weight: 40.0000 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** 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 = 0.3488 r_free = 0.3488 target = 0.065692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.055226 restraints weight = 131512.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.056393 restraints weight = 66802.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.057114 restraints weight = 42681.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.057594 restraints weight = 31994.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.057840 restraints weight = 26491.405| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12904 Z= 0.153 Angle : 0.542 9.233 18081 Z= 0.311 Chirality : 0.039 0.221 2088 Planarity : 0.004 0.054 1762 Dihedral : 19.178 158.201 3276 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 1.07 (0.25), residues: 1123 helix: 1.59 (0.21), residues: 581 sheet: 0.33 (0.52), residues: 90 loop : -0.32 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1303 TYR 0.011 0.001 TYR A 521 PHE 0.013 0.001 PHE A 626 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (12904) covalent geometry : angle 0.54223 / 0.31 (18081) hydrogen bonds : bond 0.04718 / 3.19 ( 584) hydrogen bonds : angle 4.28123 / 3.03 ( 1559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9598 (pm20) cc_final: 0.9221 (pm20) REVERT: A 415 HIS cc_start: 0.9335 (m-70) cc_final: 0.8822 (m90) REVERT: A 513 LEU cc_start: 0.8843 (mt) cc_final: 0.8495 (mt) REVERT: A 517 TYR cc_start: 0.9075 (m-80) cc_final: 0.8631 (m-80) REVERT: A 518 PHE cc_start: 0.9625 (t80) cc_final: 0.9186 (t80) REVERT: A 534 MET cc_start: 0.5592 (ttt) cc_final: 0.5169 (ttt) REVERT: A 631 MET cc_start: 0.9148 (ptp) cc_final: 0.8861 (ptp) REVERT: A 648 MET cc_start: 0.9027 (mmp) cc_final: 0.8766 (mmm) REVERT: A 668 ASN cc_start: 0.9607 (t0) cc_final: 0.9178 (m110) REVERT: A 724 ILE cc_start: 0.9348 (mt) cc_final: 0.9010 (tt) REVERT: A 751 MET cc_start: 0.9295 (mmp) cc_final: 0.8884 (mmm) REVERT: A 926 GLN cc_start: 0.9369 (mm-40) cc_final: 0.9080 (mt0) REVERT: A 943 TYR cc_start: 0.9401 (p90) cc_final: 0.9078 (p90) REVERT: A 1089 MET cc_start: 0.8872 (tpt) cc_final: 0.8562 (tpp) REVERT: A 1170 GLU cc_start: 0.9421 (tp30) cc_final: 0.9052 (tp30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1074 time to fit residues: 15.8768 Evaluate side-chains 77 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 29 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 115 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 110 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 119 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 HIS ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 HIS ** 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 = 0.3119 r_free = 0.3119 target = 0.043993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.032801 restraints weight = 138744.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033679 restraints weight = 85352.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034275 restraints weight = 61973.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.034671 restraints weight = 50000.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.034909 restraints weight = 43114.298| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 12904 Z= 0.316 Angle : 0.773 8.581 18081 Z= 0.438 Chirality : 0.045 0.240 2088 Planarity : 0.006 0.079 1762 Dihedral : 19.603 160.117 3276 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1123 helix: 0.63 (0.20), residues: 582 sheet: 0.22 (0.62), residues: 62 loop : -0.75 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 653 TYR 0.022 0.003 TYR A 521 PHE 0.023 0.003 PHE A1204 TRP 0.022 0.003 TRP A 659 HIS 0.009 0.003 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.32 (12904) covalent geometry : angle 0.77259 / 0.44 (18081) hydrogen bonds : bond 0.07836 / 5.28 ( 584) hydrogen bonds : angle 4.84972 / 3.41 ( 1559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 TYR cc_start: 0.9609 (t80) cc_final: 0.9316 (t80) REVERT: A 415 HIS cc_start: 0.9371 (m-70) cc_final: 0.8900 (m90) REVERT: A 495 MET cc_start: 0.8851 (mtm) cc_final: 0.8502 (mtp) REVERT: A 517 TYR cc_start: 0.9245 (m-80) cc_final: 0.8817 (m-80) REVERT: A 518 PHE cc_start: 0.9653 (t80) cc_final: 0.9387 (t80) REVERT: A 534 MET cc_start: 0.5955 (ttt) cc_final: 0.5600 (ttt) REVERT: A 631 MET cc_start: 0.9355 (ptp) cc_final: 0.9083 (ptp) REVERT: A 648 MET cc_start: 0.9256 (mmp) cc_final: 0.8953 (mmm) REVERT: A 668 ASN cc_start: 0.9612 (t0) cc_final: 0.9316 (m-40) REVERT: A 724 ILE cc_start: 0.9547 (mt) cc_final: 0.9283 (tt) REVERT: A 751 MET cc_start: 0.9180 (mmp) cc_final: 0.8874 (mmm) REVERT: A 943 TYR cc_start: 0.9437 (p90) cc_final: 0.9179 (p90) REVERT: A 1126 TRP cc_start: 0.9187 (m-10) cc_final: 0.8922 (m-10) REVERT: A 1170 GLU cc_start: 0.9384 (tp30) cc_final: 0.8982 (tp30) REVERT: A 1171 ARG cc_start: 0.9700 (ttt180) cc_final: 0.9415 (ttm170) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1242 time to fit residues: 15.8388 Evaluate side-chains 73 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 47 optimal weight: 0.0370 chunk 66 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 328 HIS A 690 ASN ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.064386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.054034 restraints weight = 132808.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.055260 restraints weight = 66780.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.055952 restraints weight = 41530.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.056419 restraints weight = 31246.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.056694 restraints weight = 25887.100| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12904 Z= 0.123 Angle : 0.558 10.933 18081 Z= 0.314 Chirality : 0.040 0.231 2088 Planarity : 0.004 0.053 1762 Dihedral : 19.422 160.055 3276 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1123 helix: 1.38 (0.21), residues: 580 sheet: 0.04 (0.53), residues: 89 loop : -0.45 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1303 TYR 0.011 0.001 TYR A 347 PHE 0.013 0.001 PHE A 491 TRP 0.031 0.002 TRP A 464 HIS 0.007 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (12904) covalent geometry : angle 0.55796 / 0.31 (18081) hydrogen bonds : bond 0.04050 / 2.72 ( 584) hydrogen bonds : angle 4.29961 / 3.02 ( 1559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9524 (pm20) cc_final: 0.9311 (pm20) REVERT: A 271 TYR cc_start: 0.9610 (t80) cc_final: 0.9355 (t80) REVERT: A 415 HIS cc_start: 0.9383 (m-70) cc_final: 0.8871 (m90) REVERT: A 518 PHE cc_start: 0.9562 (t80) cc_final: 0.9160 (t80) REVERT: A 534 MET cc_start: 0.5234 (ttt) cc_final: 0.4775 (ttt) REVERT: A 648 MET cc_start: 0.9079 (mmp) cc_final: 0.8826 (mmm) REVERT: A 668 ASN cc_start: 0.9521 (t0) cc_final: 0.9210 (m-40) REVERT: A 724 ILE cc_start: 0.9474 (mt) cc_final: 0.9154 (tt) REVERT: A 751 MET cc_start: 0.9092 (mmp) cc_final: 0.8781 (mmm) REVERT: A 943 TYR cc_start: 0.9417 (p90) cc_final: 0.9073 (p90) REVERT: A 1089 MET cc_start: 0.9423 (tpp) cc_final: 0.8958 (tpp) REVERT: A 1170 GLU cc_start: 0.9280 (tp30) cc_final: 0.8920 (tp30) REVERT: A 1171 ARG cc_start: 0.9684 (ttt180) cc_final: 0.9393 (ttm170) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1325 time to fit residues: 17.8472 Evaluate side-chains 73 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 50.0000 chunk 45 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 67 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 HIS ** 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 = 0.3441 r_free = 0.3441 target = 0.062655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.052326 restraints weight = 135638.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.053436 restraints weight = 68912.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.054110 restraints weight = 43939.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.054597 restraints weight = 32952.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.054868 restraints weight = 27267.501| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12904 Z= 0.153 Angle : 0.538 9.310 18081 Z= 0.314 Chirality : 0.039 0.229 2088 Planarity : 0.004 0.053 1762 Dihedral : 19.373 160.932 3276 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.77 (0.25), residues: 1123 helix: 1.41 (0.21), residues: 580 sheet: -0.04 (0.54), residues: 90 loop : -0.50 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1303 TYR 0.010 0.001 TYR A 347 PHE 0.013 0.001 PHE A 351 TRP 0.021 0.002 TRP A 464 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12904) covalent geometry : angle 0.53812 / 0.31 (18081) hydrogen bonds : bond 0.04634 / 3.15 ( 584) hydrogen bonds : angle 4.33729 / 3.05 ( 1559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9562 (pm20) cc_final: 0.9344 (pm20) REVERT: A 271 TYR cc_start: 0.9566 (t80) cc_final: 0.9290 (t80) REVERT: A 415 HIS cc_start: 0.9443 (m-70) cc_final: 0.8908 (m90) REVERT: A 518 PHE cc_start: 0.9599 (t80) cc_final: 0.9236 (t80) REVERT: A 534 MET cc_start: 0.5639 (ttt) cc_final: 0.5222 (ttt) REVERT: A 631 MET cc_start: 0.9655 (ptp) cc_final: 0.9324 (ptp) REVERT: A 648 MET cc_start: 0.9192 (mmp) cc_final: 0.8954 (mmm) REVERT: A 668 ASN cc_start: 0.9528 (t0) cc_final: 0.9295 (m-40) REVERT: A 724 ILE cc_start: 0.9473 (mt) cc_final: 0.9173 (tt) REVERT: A 751 MET cc_start: 0.9090 (mmp) cc_final: 0.8795 (mmm) REVERT: A 943 TYR cc_start: 0.9392 (p90) cc_final: 0.9066 (p90) REVERT: A 1089 MET cc_start: 0.9355 (tpp) cc_final: 0.8727 (tpt) REVERT: A 1170 GLU cc_start: 0.9313 (tp30) cc_final: 0.8974 (tp30) REVERT: A 1171 ARG cc_start: 0.9694 (ttt180) cc_final: 0.9413 (ttm170) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1274 time to fit residues: 16.5234 Evaluate side-chains 68 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** 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 = 0.3435 r_free = 0.3435 target = 0.062399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.052079 restraints weight = 136659.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.053225 restraints weight = 69245.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.053888 restraints weight = 43441.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.054361 restraints weight = 32648.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.054645 restraints weight = 27132.242| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12904 Z= 0.150 Angle : 0.538 10.674 18081 Z= 0.313 Chirality : 0.038 0.228 2088 Planarity : 0.004 0.052 1762 Dihedral : 19.373 161.355 3276 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.69 (0.24), residues: 1123 helix: 1.35 (0.21), residues: 582 sheet: -0.10 (0.53), residues: 90 loop : -0.56 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1303 TYR 0.011 0.001 TYR A 347 PHE 0.012 0.001 PHE A 351 TRP 0.011 0.001 TRP A 464 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (12904) covalent geometry : angle 0.53789 / 0.31 (18081) hydrogen bonds : bond 0.04281 / 2.90 ( 584) hydrogen bonds : angle 4.31959 / 3.04 ( 1559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9556 (pm20) cc_final: 0.9330 (pm20) REVERT: A 271 TYR cc_start: 0.9521 (t80) cc_final: 0.9262 (t80) REVERT: A 415 HIS cc_start: 0.9382 (m-70) cc_final: 0.8886 (m90) REVERT: A 518 PHE cc_start: 0.9572 (t80) cc_final: 0.9213 (t80) REVERT: A 534 MET cc_start: 0.5420 (ttt) cc_final: 0.5016 (ttt) REVERT: A 648 MET cc_start: 0.9195 (mmp) cc_final: 0.8946 (mmm) REVERT: A 724 ILE cc_start: 0.9538 (mt) cc_final: 0.9247 (tt) REVERT: A 751 MET cc_start: 0.9022 (mmp) cc_final: 0.8727 (mmm) REVERT: A 943 TYR cc_start: 0.9395 (p90) cc_final: 0.9059 (p90) REVERT: A 1089 MET cc_start: 0.9403 (tpp) cc_final: 0.8980 (tpp) REVERT: A 1170 GLU cc_start: 0.9288 (tp30) cc_final: 0.8959 (tp30) REVERT: A 1171 ARG cc_start: 0.9701 (ttt180) cc_final: 0.9414 (ttm170) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1259 time to fit residues: 16.4681 Evaluate side-chains 70 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 40 optimal weight: 7.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 HIS ** 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 = 0.3404 r_free = 0.3404 target = 0.060550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.050442 restraints weight = 137123.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051586 restraints weight = 69185.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.052203 restraints weight = 43663.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.052670 restraints weight = 33087.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.052901 restraints weight = 27337.691| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12904 Z= 0.178 Angle : 0.568 9.447 18081 Z= 0.329 Chirality : 0.039 0.226 2088 Planarity : 0.004 0.052 1762 Dihedral : 19.494 162.045 3276 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.54 (0.24), residues: 1123 helix: 1.26 (0.21), residues: 582 sheet: -0.23 (0.54), residues: 90 loop : -0.65 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1303 TYR 0.012 0.002 TYR A 347 PHE 0.016 0.002 PHE A 351 TRP 0.012 0.002 TRP A 464 HIS 0.005 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (12904) covalent geometry : angle 0.56784 / 0.33 (18081) hydrogen bonds : bond 0.05082 / 3.45 ( 584) hydrogen bonds : angle 4.38191 / 3.07 ( 1559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1866.42 seconds wall clock time: 33 minutes 13.80 seconds (1993.80 seconds total)