Starting phenix.real_space_refine on Thu Aug 6 00:50:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9waa_65810/08_2026/9waa_65810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9waa_65810/08_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_65810/08_2026/9waa_65810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9waa_65810/08_2026/9waa_65810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9waa_65810/08_2026/9waa_65810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9waa_65810/08_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-2.2rc3-6140/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: 2.40, per 1000 atoms: 0.19 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: 0.88 Conformation dependent library (CDL) restraints added in 388.6 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: 1.10 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: 2.52 Time building geometry restraints manager: 1.15 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: 17848 2.47 - 4.94: 232 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: 1369 0.032 - 0.064: 427 0.064 - 0.097: 140 0.097 - 0.129: 97 0.129 - 0.161: 55 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=" 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 2.47 2.33 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" C2' G D 35 " pdb=" C3' G D 35 " pdb=" O2' G D 35 " pdb=" C1' G D 35 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.02e-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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.900 Find NCS groups from input model: 0.060 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- 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= 0.265 Angle : 0.630 12.340 18081 Z= 0.499 Chirality : 0.046 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 0.00310 / 0.27 (12904) covalent geometry : angle 0.63045 / 0.50 (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 : 0.314 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: 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: 0.7564 (t) REVERT: A 515 TYR cc_start: 0.8839 (t80) cc_final: 0.8395 (t80) 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: 0.8727 (mt) REVERT: A 668 ASN cc_start: 0.9382 (t0) cc_final: 0.9162 (m110) REVERT: A 1135 ASP cc_start: 0.7374 (t0) cc_final: 0.7013 (t70) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1263 time to fit residues: 34.4399 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 : 0.286 ------------------------------------------------------------------------------- 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: 40.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 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 ** A1264 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 = 0.3333 r_free = 0.3333 target = 0.050536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037402 restraints weight = 109546.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038479 restraints weight = 66895.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.039185 restraints weight = 48326.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039619 restraints weight = 38820.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039943 restraints weight = 33631.335| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12904 Z= 0.214 Angle : 0.658 8.144 18081 Z= 0.368 Chirality : 0.043 0.211 2088 Planarity : 0.005 0.063 1762 Dihedral : 18.845 154.610 3276 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 1.09 (0.24), residues: 1123 helix: 1.50 (0.21), residues: 582 sheet: 1.05 (0.54), residues: 90 loop : -0.31 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 557 TYR 0.016 0.002 TYR A 594 PHE 0.017 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 0.00407 / 0.21 (12904) covalent geometry : angle 0.65817 / 0.37 (18081) hydrogen bonds : bond 0.05796 / 3.97 ( 584) hydrogen bonds : angle 4.68557 / 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 128 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.341 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: 0.9564 (pm20) cc_final: 0.9303 (pm20) REVERT: A 75 ARG cc_start: 0.9660 (tmm160) cc_final: 0.9392 (mmt-90) REVERT: A 415 HIS cc_start: 0.9428 (m90) cc_final: 0.9013 (m90) REVERT: A 517 TYR cc_start: 0.9058 (m-80) cc_final: 0.8723 (m-80) REVERT: A 518 PHE cc_start: 0.9612 (t80) cc_final: 0.9167 (t80) REVERT: A 668 ASN cc_start: 0.9580 (t0) cc_final: 0.9285 (m-40) REVERT: A 724 ILE cc_start: 0.9271 (mt) cc_final: 0.8939 (tt) REVERT: A 751 MET cc_start: 0.9446 (mmp) cc_final: 0.8946 (mmm) REVERT: A 926 GLN cc_start: 0.9416 (mm-40) cc_final: 0.8953 (mt0) REVERT: A 943 TYR cc_start: 0.9437 (p90) cc_final: 0.9230 (p90) REVERT: A 1089 MET cc_start: 0.8782 (tpt) cc_final: 0.7931 (tpp) REVERT: A 1126 TRP cc_start: 0.9108 (m-10) cc_final: 0.8803 (m-10) REVERT: A 1170 GLU cc_start: 0.9481 (tp30) cc_final: 0.9238 (tm-30) REVERT: A 1171 ARG cc_start: 0.9704 (ttt180) cc_final: 0.9403 (ttm170) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1226 time to fit residues: 21.7110 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 : 0.394 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 115 optimal weight: 40.0000 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A1101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054679 restraints weight = 133081.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.055883 restraints weight = 68227.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.056584 restraints weight = 43568.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.057077 restraints weight = 33051.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057368 restraints weight = 27425.210| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12904 Z= 0.262 Angle : 0.686 8.313 18081 Z= 0.391 Chirality : 0.042 0.264 2088 Planarity : 0.005 0.063 1762 Dihedral : 19.147 153.893 3276 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 0.74 (0.24), residues: 1123 helix: 1.25 (0.21), residues: 574 sheet: 1.16 (0.63), residues: 59 loop : -0.46 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1303 TYR 0.022 0.002 TYR A1201 PHE 0.022 0.002 PHE A 626 TRP 0.013 0.002 TRP A 476 HIS 0.009 0.002 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.26 (12904) covalent geometry : angle 0.68572 / 0.39 (18081) hydrogen bonds : bond 0.06158 / 4.14 ( 584) hydrogen bonds : angle 4.71067 / 3.36 ( 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 111 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.293 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: 0.9558 (pm20) cc_final: 0.9315 (pm20) REVERT: A 275 LEU cc_start: 0.9594 (mm) cc_final: 0.9390 (mt) REVERT: A 415 HIS cc_start: 0.9369 (m90) cc_final: 0.8978 (m90) REVERT: A 517 TYR cc_start: 0.9086 (m-80) cc_final: 0.8702 (m-80) REVERT: A 518 PHE cc_start: 0.9641 (t80) cc_final: 0.9115 (t80) REVERT: A 534 MET cc_start: 0.5860 (ttt) cc_final: 0.5402 (ttt) REVERT: A 596 ASP cc_start: 0.9014 (m-30) cc_final: 0.8756 (m-30) REVERT: A 668 ASN cc_start: 0.9598 (t0) cc_final: 0.9247 (m-40) REVERT: A 724 ILE cc_start: 0.9327 (mt) cc_final: 0.8980 (tt) REVERT: A 751 MET cc_start: 0.9370 (mmp) cc_final: 0.8923 (mmm) REVERT: A 943 TYR cc_start: 0.9391 (p90) cc_final: 0.9082 (p90) REVERT: A 1126 TRP cc_start: 0.9129 (m-10) cc_final: 0.8865 (m-10) REVERT: A 1170 GLU cc_start: 0.9441 (tp30) cc_final: 0.9192 (tm-30) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1064 time to fit residues: 17.0071 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 : 0.389 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 115 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 9 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** 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 = 0.3501 r_free = 0.3501 target = 0.066632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.056041 restraints weight = 130389.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.057215 restraints weight = 66620.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.057951 restraints weight = 42725.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.058430 restraints weight = 32042.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.058739 restraints weight = 26456.702| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.003 0.045 12904 Z= 0.150 Angle : 0.548 9.056 18081 Z= 0.320 Chirality : 0.040 0.226 2088 Planarity : 0.004 0.059 1762 Dihedral : 19.208 154.813 3276 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.10 % Allowed : 1.49 % Favored : 98.41 % 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: 0.89 (0.25), residues: 1123 helix: 1.45 (0.21), residues: 576 sheet: 0.33 (0.53), residues: 90 loop : -0.40 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1303 TYR 0.014 0.002 TYR A 430 PHE 0.012 0.001 PHE A 626 TRP 0.007 0.001 TRP A 476 HIS 0.008 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (12904) covalent geometry : angle 0.54825 / 0.32 (18081) hydrogen bonds : bond 0.04643 / 3.14 ( 584) hydrogen bonds : angle 4.42787 / 3.15 ( 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 106 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.348 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: 0.9545 (pm20) cc_final: 0.9277 (pm20) REVERT: A 415 HIS cc_start: 0.9304 (m-70) cc_final: 0.8860 (m90) REVERT: A 517 TYR cc_start: 0.9063 (m-80) cc_final: 0.8660 (m-80) REVERT: A 518 PHE cc_start: 0.9570 (t80) cc_final: 0.9032 (t80) REVERT: A 534 MET cc_start: 0.5606 (ttt) cc_final: 0.5158 (ttt) REVERT: A 648 MET cc_start: 0.8936 (mmp) cc_final: 0.8705 (mmm) REVERT: A 668 ASN cc_start: 0.9519 (t0) cc_final: 0.9162 (m-40) REVERT: A 724 ILE cc_start: 0.9316 (mt) cc_final: 0.8970 (tt) REVERT: A 751 MET cc_start: 0.9344 (mmp) cc_final: 0.8910 (mmm) REVERT: A 926 GLN cc_start: 0.9375 (mp-120) cc_final: 0.9024 (tp40) REVERT: A 943 TYR cc_start: 0.9393 (p90) cc_final: 0.9082 (p90) REVERT: A 1089 MET cc_start: 0.9122 (tpt) cc_final: 0.7996 (tpp) REVERT: A 1170 GLU cc_start: 0.9385 (tp30) cc_final: 0.8996 (tp30) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1027 time to fit residues: 15.5913 Evaluate side-chains 76 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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: 7.9990 chunk 121 optimal weight: 50.0000 chunk 60 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 HIS A 556 ASN ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 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 = 0.3454 r_free = 0.3454 target = 0.063788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.053377 restraints weight = 134557.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.054554 restraints weight = 68090.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.055233 restraints weight = 43459.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.055700 restraints weight = 32934.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.055986 restraints weight = 27424.706| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12904 Z= 0.212 Angle : 0.619 8.810 18081 Z= 0.352 Chirality : 0.041 0.244 2088 Planarity : 0.005 0.066 1762 Dihedral : 19.276 156.739 3276 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.10 % Allowed : 1.09 % Favored : 98.81 % 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: 0.61 (0.24), residues: 1123 helix: 1.17 (0.21), residues: 578 sheet: 0.59 (0.60), residues: 62 loop : -0.49 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 74 TYR 0.015 0.002 TYR A 521 PHE 0.016 0.002 PHE A 626 TRP 0.012 0.002 TRP A 476 HIS 0.007 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 (12904) covalent geometry : angle 0.61922 / 0.35 (18081) hydrogen bonds : bond 0.05641 / 3.78 ( 584) hydrogen bonds : angle 4.51236 / 3.20 ( 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 96 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.356 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: 0.9563 (pm20) cc_final: 0.9275 (pm20) REVERT: A 415 HIS cc_start: 0.9366 (m-70) cc_final: 0.8922 (m90) REVERT: A 517 TYR cc_start: 0.9125 (m-80) cc_final: 0.8748 (m-80) REVERT: A 518 PHE cc_start: 0.9617 (t80) cc_final: 0.9124 (t80) REVERT: A 534 MET cc_start: 0.5865 (ttt) cc_final: 0.5455 (ttt) REVERT: A 628 ASP cc_start: 0.9728 (t70) cc_final: 0.9467 (t70) REVERT: A 631 MET cc_start: 0.9082 (ptp) cc_final: 0.8512 (ptp) REVERT: A 648 MET cc_start: 0.9061 (mmp) cc_final: 0.8767 (mmm) REVERT: A 668 ASN cc_start: 0.9549 (t0) cc_final: 0.9168 (m-40) REVERT: A 724 ILE cc_start: 0.9387 (mt) cc_final: 0.9048 (tt) REVERT: A 751 MET cc_start: 0.9317 (mmp) cc_final: 0.8902 (mmm) REVERT: A 943 TYR cc_start: 0.9381 (p90) cc_final: 0.9060 (p90) REVERT: A 1170 GLU cc_start: 0.9372 (tp30) cc_final: 0.8985 (tp30) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.0983 time to fit residues: 13.8319 Evaluate side-chains 75 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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: 30.0000 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 120 optimal weight: 50.0000 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN ** A 698 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 = 0.3437 r_free = 0.3437 target = 0.062637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.052414 restraints weight = 135330.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.053577 restraints weight = 68285.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.054224 restraints weight = 42898.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.054669 restraints weight = 32493.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.054929 restraints weight = 27010.770| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5070 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= 0.192 Angle : 0.585 8.158 18081 Z= 0.338 Chirality : 0.041 0.242 2088 Planarity : 0.004 0.055 1762 Dihedral : 19.419 157.745 3276 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.59 (0.24), residues: 1123 helix: 1.18 (0.21), residues: 581 sheet: 0.18 (0.60), residues: 62 loop : -0.48 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 75 TYR 0.018 0.002 TYR A 521 PHE 0.015 0.002 PHE A 351 TRP 0.013 0.002 TRP A 476 HIS 0.012 0.002 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 (12904) covalent geometry : angle 0.58519 / 0.34 (18081) hydrogen bonds : bond 0.04799 / 3.24 ( 584) hydrogen bonds : angle 4.46565 / 3.15 ( 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 93 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.260 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: 0.9634 (pm20) cc_final: 0.9303 (pm20) REVERT: A 415 HIS cc_start: 0.9440 (m-70) cc_final: 0.8978 (m90) REVERT: A 517 TYR cc_start: 0.9106 (m-80) cc_final: 0.8781 (m-80) REVERT: A 518 PHE cc_start: 0.9625 (t80) cc_final: 0.9128 (t80) REVERT: A 534 MET cc_start: 0.5681 (ttt) cc_final: 0.5257 (ttt) REVERT: A 628 ASP cc_start: 0.9748 (t70) cc_final: 0.9520 (t70) REVERT: A 631 MET cc_start: 0.9183 (ptp) cc_final: 0.8689 (ptp) REVERT: A 648 MET cc_start: 0.9090 (mmp) cc_final: 0.8830 (mmm) REVERT: A 668 ASN cc_start: 0.9568 (t0) cc_final: 0.9236 (m-40) REVERT: A 724 ILE cc_start: 0.9453 (mt) cc_final: 0.9141 (tt) REVERT: A 751 MET cc_start: 0.9182 (mmp) cc_final: 0.8818 (mmm) REVERT: A 943 TYR cc_start: 0.9400 (p90) cc_final: 0.9070 (p90) REVERT: A 1170 GLU cc_start: 0.9305 (tp30) cc_final: 0.8942 (tp30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0979 time to fit residues: 13.0729 Evaluate side-chains 71 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 20.0000 chunk 36 optimal weight: 9.9990 chunk 115 optimal weight: 40.0000 chunk 81 optimal weight: 8.9990 chunk 124 optimal weight: 50.0000 chunk 110 optimal weight: 7.9990 chunk 26 optimal weight: 50.0000 chunk 119 optimal weight: 50.0000 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN ** 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 = 0.3124 r_free = 0.3124 target = 0.044146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.032812 restraints weight = 138607.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033706 restraints weight = 84807.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.034263 restraints weight = 61844.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.034649 restraints weight = 50309.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.034801 restraints weight = 43768.245| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12904 Z= 0.261 Angle : 0.678 8.575 18081 Z= 0.387 Chirality : 0.043 0.264 2088 Planarity : 0.005 0.056 1762 Dihedral : 19.627 158.753 3276 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -0.07 (0.24), residues: 1123 helix: 0.58 (0.20), residues: 585 sheet: 0.23 (0.62), residues: 59 loop : -0.78 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 457 TYR 0.014 0.002 TYR A 347 PHE 0.024 0.002 PHE A1276 TRP 0.016 0.002 TRP A 659 HIS 0.008 0.002 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.26 (12904) covalent geometry : angle 0.67812 / 0.39 (18081) hydrogen bonds : bond 0.06715 / 4.54 ( 584) hydrogen bonds : angle 4.73024 / 3.33 ( 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 86 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.331 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 1 MET cc_start: 0.6514 (ttp) cc_final: 0.6141 (tmm) REVERT: A 54 ASP cc_start: 0.9323 (m-30) cc_final: 0.9086 (m-30) REVERT: A 60 GLU cc_start: 0.9669 (pm20) cc_final: 0.9364 (pm20) REVERT: A 399 LEU cc_start: 0.9780 (pp) cc_final: 0.9570 (mt) REVERT: A 415 HIS cc_start: 0.9340 (m-70) cc_final: 0.8908 (m90) REVERT: A 518 PHE cc_start: 0.9536 (t80) cc_final: 0.9159 (t80) REVERT: A 534 MET cc_start: 0.6099 (ttt) cc_final: 0.5771 (ttt) REVERT: A 648 MET cc_start: 0.9270 (mmp) cc_final: 0.8969 (mmm) REVERT: A 668 ASN cc_start: 0.9638 (t0) cc_final: 0.9430 (m110) REVERT: A 724 ILE cc_start: 0.9565 (mt) cc_final: 0.9311 (tt) REVERT: A 943 TYR cc_start: 0.9426 (p90) cc_final: 0.9154 (p90) REVERT: A 1126 TRP cc_start: 0.9179 (m-10) cc_final: 0.8907 (m-10) REVERT: A 1170 GLU cc_start: 0.9269 (tp30) cc_final: 0.8901 (tp30) REVERT: A 1171 ARG cc_start: 0.9702 (ttt180) cc_final: 0.9434 (ttm170) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1020 time to fit residues: 12.7792 Evaluate side-chains 65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 6.9990 chunk 66 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 23 optimal weight: 0.0020 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 ASN ** 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 = 0.3439 r_free = 0.3439 target = 0.062590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.052266 restraints weight = 135601.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.053452 restraints weight = 67892.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.054147 restraints weight = 42397.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.054539 restraints weight = 31695.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.054816 restraints weight = 26645.869| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12904 Z= 0.131 Angle : 0.555 10.388 18081 Z= 0.318 Chirality : 0.040 0.248 2088 Planarity : 0.004 0.053 1762 Dihedral : 19.550 158.939 3276 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 0.38 (0.24), residues: 1123 helix: 1.13 (0.21), residues: 583 sheet: -0.47 (0.53), residues: 93 loop : -0.69 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1303 TYR 0.021 0.002 TYR A 517 PHE 0.027 0.002 PHE A1276 TRP 0.004 0.001 TRP A 464 HIS 0.008 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (12904) covalent geometry : angle 0.55523 / 0.32 (18081) hydrogen bonds : bond 0.04213 / 2.85 ( 584) hydrogen bonds : angle 4.40707 / 3.10 ( 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 93 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6434 (ttp) cc_final: 0.6130 (tmm) REVERT: A 60 GLU cc_start: 0.9630 (pm20) cc_final: 0.9311 (pm20) REVERT: A 371 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9183 (mt-10) REVERT: A 415 HIS cc_start: 0.9460 (m-70) cc_final: 0.8987 (m90) REVERT: A 517 TYR cc_start: 0.9129 (m-80) cc_final: 0.8630 (m-80) REVERT: A 518 PHE cc_start: 0.9569 (t80) cc_final: 0.9121 (t80) REVERT: A 534 MET cc_start: 0.5695 (ttt) cc_final: 0.5303 (ttt) REVERT: A 648 MET cc_start: 0.9176 (mmp) cc_final: 0.8935 (mmm) REVERT: A 668 ASN cc_start: 0.9550 (t0) cc_final: 0.9309 (m-40) REVERT: A 724 ILE cc_start: 0.9507 (mt) cc_final: 0.9203 (tt) REVERT: A 943 TYR cc_start: 0.9408 (p90) cc_final: 0.9088 (p90) REVERT: A 1089 MET cc_start: 0.8972 (tpt) cc_final: 0.8175 (tpt) REVERT: A 1170 GLU cc_start: 0.9166 (tp30) cc_final: 0.8765 (tp30) REVERT: A 1171 ARG cc_start: 0.9676 (ttt180) cc_final: 0.9401 (ttm170) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0969 time to fit residues: 12.9770 Evaluate side-chains 72 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 6.9990 chunk 78 optimal weight: 0.0970 chunk 61 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 50.0000 chunk 45 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 67 optimal weight: 0.0870 overall best weight: 3.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 ASN ** 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 = 0.3440 r_free = 0.3440 target = 0.062484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.052196 restraints weight = 135984.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.053386 restraints weight = 68122.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.054023 restraints weight = 42341.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.054480 restraints weight = 31995.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.054751 restraints weight = 26589.551| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12904 Z= 0.132 Angle : 0.540 10.553 18081 Z= 0.309 Chirality : 0.039 0.240 2088 Planarity : 0.004 0.052 1762 Dihedral : 19.500 159.587 3276 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.51 (0.25), residues: 1123 helix: 1.25 (0.21), residues: 581 sheet: -0.33 (0.53), residues: 93 loop : -0.66 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1303 TYR 0.015 0.001 TYR A 517 PHE 0.022 0.001 PHE A1276 TRP 0.006 0.001 TRP A 464 HIS 0.007 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (12904) covalent geometry : angle 0.53952 / 0.31 (18081) hydrogen bonds : bond 0.04225 / 2.86 ( 584) hydrogen bonds : angle 4.34737 / 3.06 ( 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 89 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 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: A 1 MET cc_start: 0.6393 (ttp) cc_final: 0.6130 (tmm) REVERT: A 60 GLU cc_start: 0.9645 (pm20) cc_final: 0.9314 (pm20) REVERT: A 371 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9183 (mt-10) REVERT: A 415 HIS cc_start: 0.9454 (m-70) cc_final: 0.8988 (m90) REVERT: A 518 PHE cc_start: 0.9523 (t80) cc_final: 0.9130 (t80) REVERT: A 534 MET cc_start: 0.5508 (ttt) cc_final: 0.5101 (ttt) REVERT: A 631 MET cc_start: 0.9606 (ptp) cc_final: 0.9296 (ptm) REVERT: A 648 MET cc_start: 0.9172 (mmp) cc_final: 0.8948 (mmm) REVERT: A 668 ASN cc_start: 0.9576 (t0) cc_final: 0.9302 (m110) REVERT: A 724 ILE cc_start: 0.9497 (mt) cc_final: 0.9205 (tt) REVERT: A 943 TYR cc_start: 0.9409 (p90) cc_final: 0.9083 (p90) REVERT: A 1089 MET cc_start: 0.8956 (tpt) cc_final: 0.8179 (tpt) REVERT: A 1135 ASP cc_start: 0.9325 (m-30) cc_final: 0.9121 (m-30) REVERT: A 1170 GLU cc_start: 0.9200 (tp30) cc_final: 0.8807 (tp30) REVERT: A 1171 ARG cc_start: 0.9676 (ttt180) cc_final: 0.9409 (ttm170) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0930 time to fit residues: 12.1022 Evaluate side-chains 69 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3418 r_free = 0.3418 target = 0.061279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.050960 restraints weight = 138354.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.052082 restraints weight = 69732.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052791 restraints weight = 44528.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.053237 restraints weight = 33313.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.053499 restraints weight = 27663.636| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12904 Z= 0.152 Angle : 0.548 9.620 18081 Z= 0.314 Chirality : 0.038 0.234 2088 Planarity : 0.004 0.052 1762 Dihedral : 19.536 159.411 3276 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % 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: 0.47 (0.25), residues: 1123 helix: 1.21 (0.21), residues: 586 sheet: -0.28 (0.54), residues: 93 loop : -0.70 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1303 TYR 0.011 0.001 TYR A 347 PHE 0.022 0.002 PHE A1276 TRP 0.009 0.001 TRP A 464 HIS 0.007 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (12904) covalent geometry : angle 0.54766 / 0.31 (18081) hydrogen bonds : bond 0.04544 / 3.08 ( 584) hydrogen bonds : angle 4.35615 / 3.07 ( 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 85 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6504 (ttp) cc_final: 0.6260 (tmm) REVERT: A 60 GLU cc_start: 0.9624 (pm20) cc_final: 0.9310 (pm20) REVERT: A 271 TYR cc_start: 0.9509 (t80) cc_final: 0.9213 (t80) REVERT: A 371 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9102 (mt-10) REVERT: A 415 HIS cc_start: 0.9384 (m-70) cc_final: 0.8950 (m90) REVERT: A 518 PHE cc_start: 0.9524 (t80) cc_final: 0.9148 (t80) REVERT: A 534 MET cc_start: 0.5376 (ttt) cc_final: 0.4951 (ttt) REVERT: A 631 MET cc_start: 0.9642 (ptp) cc_final: 0.9271 (ptm) REVERT: A 648 MET cc_start: 0.9134 (mmp) cc_final: 0.8864 (mmm) REVERT: A 668 ASN cc_start: 0.9572 (t0) cc_final: 0.9362 (m110) REVERT: A 724 ILE cc_start: 0.9517 (mt) cc_final: 0.9227 (tt) REVERT: A 943 TYR cc_start: 0.9346 (p90) cc_final: 0.8983 (p90) REVERT: A 1089 MET cc_start: 0.8957 (tpt) cc_final: 0.8331 (tpt) REVERT: A 1170 GLU cc_start: 0.9183 (tp30) cc_final: 0.8786 (tp30) REVERT: A 1171 ARG cc_start: 0.9674 (ttt180) cc_final: 0.9417 (ttm170) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0953 time to fit residues: 11.8946 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 : 0.312 ------------------------------------------------------------------------------- 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: 0.0570 chunk 85 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 40.0000 chunk 16 optimal weight: 0.0370 chunk 27 optimal weight: 40.0000 chunk 88 optimal weight: 6.9990 chunk 119 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3424 r_free = 0.3424 target = 0.061617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051394 restraints weight = 135523.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.052493 restraints weight = 68163.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.053174 restraints weight = 43555.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.053617 restraints weight = 32641.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.053876 restraints weight = 27211.106| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12904 Z= 0.138 Angle : 0.527 10.025 18081 Z= 0.302 Chirality : 0.038 0.233 2088 Planarity : 0.004 0.051 1762 Dihedral : 19.538 159.552 3276 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % 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: 0.52 (0.24), residues: 1123 helix: 1.29 (0.21), residues: 585 sheet: -0.29 (0.54), residues: 93 loop : -0.74 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1303 TYR 0.017 0.001 TYR A 517 PHE 0.022 0.001 PHE A1276 TRP 0.005 0.001 TRP A 464 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (12904) covalent geometry : angle 0.52699 / 0.30 (18081) hydrogen bonds : bond 0.04188 / 2.83 ( 584) hydrogen bonds : angle 4.30176 / 3.03 ( 1559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1568.64 seconds wall clock time: 28 minutes 1.10 seconds (1681.10 seconds total)