Starting phenix.real_space_refine on Wed Aug 5 20:40:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9d_65771/08_2026/9w9d_65771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9d_65771/08_2026/9w9d_65771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9d_65771/08_2026/9w9d_65771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9d_65771/08_2026/9w9d_65771.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9d_65771/08_2026/9w9d_65771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9d_65771/08_2026/9w9d_65771.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 148 5.49 5 S 18 5.16 5 C 6757 2.51 5 N 2026 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 11479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8301 Classifications: {'peptide': 1014} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 987} Chain breaks: 3 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: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2131 Classifications: {'RNA': 100} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 40} Link IDs: {'rna2p': 11, 'rna3p': 88} Time building chain proxies: 2.06, per 1000 atoms: 0.18 Number of scatterers: 11479 At special positions: 0 Unit cell: (121.362, 118.14, 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 148 15.00 O 2530 8.00 N 2026 7.00 C 6757 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: 0.68 Conformation dependent library (CDL) restraints added in 323.0 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 54.6% alpha, 8.4% beta 58 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.358A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.310A pdb=" N HIS A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.544A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.648A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.782A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 381 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.958A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.937A 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 477 through 482 removed outlier: 3.594A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.988A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.280A 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 603 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 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.640A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.163A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.270A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.572A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.549A pdb=" N LYS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.854A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.514A pdb=" N ASN A1295 " --> pdb=" O LEU A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 4.231A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 956 removed outlier: 6.385A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 760 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 19 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A1093 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.955A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A1348 " --> pdb=" O LEU A1203 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.951A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.721A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326 384 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 292 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2566 1.33 - 1.45: 3170 1.45 - 1.57: 5947 1.57 - 1.69: 296 1.69 - 1.81: 34 Bond restraints: 12013 Sorted by residual: bond pdb=" C3' DG C 3 " pdb=" C2' DG C 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA C 13 " pdb=" C2' DA C 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC B 16 " pdb=" C2' DC B 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 bond pdb=" C3' DG B 7 " pdb=" C2' DG B 7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.31e+00 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.27e+00 ... (remaining 12008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 16109 1.49 - 2.98: 736 2.98 - 4.48: 28 4.48 - 5.97: 4 5.97 - 7.46: 2 Bond angle restraints: 16879 Sorted by residual: angle pdb=" O4' DG B 23 " pdb=" C4' DG B 23 " pdb=" C3' DG B 23 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.25e+01 angle pdb=" O4' DG B 18 " pdb=" C4' DG B 18 " pdb=" C3' DG B 18 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.80e+01 angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" O4' DC B 29 " pdb=" C4' DC B 29 " pdb=" C3' DC B 29 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" O4' DC B 30 " pdb=" C4' DC B 30 " pdb=" C3' DC B 30 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 ... (remaining 16874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.00: 6832 32.00 - 64.00: 384 64.00 - 96.00: 32 96.00 - 128.00: 0 128.00 - 160.00: 1 Dihedral angle restraints: 7249 sinusoidal: 4271 harmonic: 2978 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 60.00 160.00 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA ASP A 288 " pdb=" CB ASP A 288 " pdb=" CG ASP A 288 " pdb=" OD1 ASP A 288 " ideal model delta sinusoidal sigma weight residual -30.00 -86.95 56.95 1 2.00e+01 2.50e-03 1.09e+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 -180.00 -135.45 -44.55 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 7246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1224 0.030 - 0.059: 398 0.059 - 0.089: 154 0.089 - 0.119: 88 0.119 - 0.148: 89 Chirality restraints: 1953 Sorted by residual: chirality pdb=" P DA B 8 " pdb=" OP1 DA B 8 " pdb=" OP2 DA B 8 " pdb=" O5' DA B 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-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 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" C2' U D 73 " pdb=" C3' U D 73 " pdb=" O2' U D 73 " pdb=" C1' U D 73 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1950 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U D 99 " -0.030 2.00e-02 2.50e+03 1.45e-02 4.73e+00 pdb=" N1 U D 99 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U D 99 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U D 99 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U D 99 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U D 99 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U D 99 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U D 99 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U D 99 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 98 " -0.021 2.00e-02 2.50e+03 1.09e-02 2.66e+00 pdb=" N1 C D 98 " 0.023 2.00e-02 2.50e+03 pdb=" C2 C D 98 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C D 98 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C D 98 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C D 98 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C D 98 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C D 98 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C D 98 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A1229 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " -0.022 5.00e-02 4.00e+02 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 988 2.74 - 3.46: 16308 3.46 - 4.18: 29983 4.18 - 4.90: 46910 Nonbonded interactions: 94194 Sorted by model distance: nonbonded pdb=" NZ LYS A 742 " pdb=" OP1 C D 69 " model vdw 1.296 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" N4 C D 20 " model vdw 1.352 3.200 nonbonded pdb=" O GLY A 582 " pdb=" C4' DT B 33 " model vdw 1.378 3.470 nonbonded pdb=" CG GLN A 695 " pdb=" O3' DC B 35 " model vdw 1.380 3.440 nonbonded pdb=" O GLY A 582 " pdb=" C5' DT B 33 " model vdw 1.841 3.440 ... (remaining 94189 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: 0.430 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.500 Find NCS groups from input model: 0.030 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 0.040 12013 Z= 0.291 Angle : 0.639 7.461 16879 Z= 0.511 Chirality : 0.047 0.148 1953 Planarity : 0.003 0.040 1596 Dihedral : 16.944 159.996 5321 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.81 (0.27), residues: 1006 helix: 2.10 (0.23), residues: 501 sheet: 1.03 (0.61), residues: 69 loop : 0.23 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.011 0.001 TYR A1242 PHE 0.013 0.001 PHE A 970 TRP 0.011 0.002 TRP A 464 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.29 (12013) covalent geometry : angle 0.63923 / 0.51 (16879) hydrogen bonds : bond 0.14342 / 9.73 ( 532) hydrogen bonds : angle 5.35664 / 3.91 ( 1414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.215 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 515 TYR cc_start: 0.8891 (t80) cc_final: 0.8445 (t80) REVERT: A 662 LEU cc_start: 0.9049 (mt) cc_final: 0.8547 (mt) REVERT: A 744 VAL cc_start: 0.9741 (t) cc_final: 0.9474 (t) REVERT: A 954 LYS cc_start: 0.9421 (mttt) cc_final: 0.9038 (mmtm) REVERT: A 1317 ASN cc_start: 0.8712 (m-40) cc_final: 0.8410 (m-40) REVERT: A 1357 GLU cc_start: 0.7878 (pt0) cc_final: 0.7580 (pm20) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1277 time to fit residues: 29.2564 Evaluate side-chains 101 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 overall best weight: 6.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A 739 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.058953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.049977 restraints weight = 139647.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.051198 restraints weight = 78820.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.051994 restraints weight = 53967.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.052549 restraints weight = 41194.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.052889 restraints weight = 33688.534| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12013 Z= 0.209 Angle : 0.652 9.955 16879 Z= 0.366 Chirality : 0.042 0.217 1953 Planarity : 0.005 0.063 1596 Dihedral : 19.239 160.364 3169 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.26), residues: 1006 helix: 1.62 (0.23), residues: 517 sheet: 1.65 (0.65), residues: 59 loop : -0.13 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 63 TYR 0.020 0.002 TYR A 136 PHE 0.017 0.002 PHE A 98 TRP 0.015 0.001 TRP A 659 HIS 0.013 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.21 (12013) covalent geometry : angle 0.65164 / 0.37 (16879) hydrogen bonds : bond 0.05943 / 4.02 ( 532) hydrogen bonds : angle 4.71229 / 3.38 ( 1414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.248 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 32 PHE cc_start: 0.8675 (m-10) cc_final: 0.8377 (m-10) REVERT: A 82 LEU cc_start: 0.9862 (tt) cc_final: 0.9508 (tt) REVERT: A 86 PHE cc_start: 0.9747 (m-80) cc_final: 0.9542 (m-10) REVERT: A 90 MET cc_start: 0.9023 (ppp) cc_final: 0.8648 (ttp) REVERT: A 163 LYS cc_start: 0.9407 (ptpp) cc_final: 0.9096 (pttp) REVERT: A 450 TYR cc_start: 0.9176 (p90) cc_final: 0.8635 (p90) REVERT: A 501 ASN cc_start: 0.9101 (p0) cc_final: 0.8898 (p0) REVERT: A 587 PHE cc_start: 0.9425 (m-10) cc_final: 0.9216 (m-10) REVERT: A 1089 MET cc_start: 0.7525 (tpp) cc_final: 0.7270 (tpp) REVERT: A 1099 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9230 (mp0) REVERT: A 1204 PHE cc_start: 0.9810 (m-80) cc_final: 0.9356 (m-80) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1146 time to fit residues: 16.1190 Evaluate side-chains 81 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN ** A1317 ASN ** 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 = 0.3396 r_free = 0.3396 target = 0.055850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.047147 restraints weight = 144477.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.048316 restraints weight = 80820.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.049079 restraints weight = 55390.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.049599 restraints weight = 42439.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.049928 restraints weight = 34952.623| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12013 Z= 0.194 Angle : 0.592 7.222 16879 Z= 0.342 Chirality : 0.041 0.239 1953 Planarity : 0.005 0.061 1596 Dihedral : 19.404 158.050 3169 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 0.95 (0.26), residues: 1006 helix: 1.31 (0.22), residues: 519 sheet: 1.56 (0.66), residues: 57 loop : -0.27 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 63 TYR 0.014 0.002 TYR A 72 PHE 0.024 0.002 PHE A 693 TRP 0.013 0.002 TRP A 659 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (12013) covalent geometry : angle 0.59241 / 0.34 (16879) hydrogen bonds : bond 0.05798 / 3.95 ( 532) hydrogen bonds : angle 4.58895 / 3.28 ( 1414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.300 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 32 PHE cc_start: 0.8677 (m-10) cc_final: 0.8281 (m-10) REVERT: A 82 LEU cc_start: 0.9846 (tt) cc_final: 0.9489 (tt) REVERT: A 86 PHE cc_start: 0.9753 (m-10) cc_final: 0.9496 (m-80) REVERT: A 90 MET cc_start: 0.9357 (ppp) cc_final: 0.8675 (ttt) REVERT: A 161 MET cc_start: 0.9876 (ttt) cc_final: 0.9304 (tpt) REVERT: A 163 LYS cc_start: 0.9383 (ptpp) cc_final: 0.9001 (pttp) REVERT: A 164 PHE cc_start: 0.9575 (m-10) cc_final: 0.9206 (m-10) REVERT: A 450 TYR cc_start: 0.9159 (p90) cc_final: 0.8653 (p90) REVERT: A 587 PHE cc_start: 0.9484 (m-10) cc_final: 0.9092 (m-80) REVERT: A 694 MET cc_start: 0.9210 (tpt) cc_final: 0.8852 (tpp) REVERT: A 698 HIS cc_start: 0.8387 (m90) cc_final: 0.8109 (m170) REVERT: A 1089 MET cc_start: 0.7467 (tpp) cc_final: 0.7140 (tpp) REVERT: A 1099 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9274 (mp0) REVERT: A 1134 PHE cc_start: 0.9711 (m-80) cc_final: 0.9488 (m-80) REVERT: A 1204 PHE cc_start: 0.9833 (m-80) cc_final: 0.9410 (m-80) REVERT: A 1213 MET cc_start: 0.9687 (tpt) cc_final: 0.9435 (tpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0966 time to fit residues: 12.7551 Evaluate side-chains 76 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 107 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 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 = 0.3408 r_free = 0.3408 target = 0.056436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.047698 restraints weight = 143068.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.048877 restraints weight = 79490.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.049619 restraints weight = 54538.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.050167 restraints weight = 42135.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.050492 restraints weight = 34588.074| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12013 Z= 0.135 Angle : 0.518 6.639 16879 Z= 0.303 Chirality : 0.039 0.229 1953 Planarity : 0.004 0.057 1596 Dihedral : 19.411 157.708 3169 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 1.06 (0.26), residues: 1006 helix: 1.41 (0.23), residues: 518 sheet: 1.59 (0.64), residues: 57 loop : -0.23 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 63 TYR 0.011 0.001 TYR A 128 PHE 0.012 0.001 PHE A 970 TRP 0.004 0.001 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (12013) covalent geometry : angle 0.51816 / 0.30 (16879) hydrogen bonds : bond 0.04319 / 2.99 ( 532) hydrogen bonds : angle 4.36530 / 3.10 ( 1414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.325 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 32 PHE cc_start: 0.8632 (m-10) cc_final: 0.8266 (m-10) REVERT: A 90 MET cc_start: 0.9341 (ppp) cc_final: 0.9017 (ttp) REVERT: A 161 MET cc_start: 0.9859 (ttt) cc_final: 0.9360 (tpp) REVERT: A 163 LYS cc_start: 0.9363 (ptpp) cc_final: 0.9072 (pttp) REVERT: A 164 PHE cc_start: 0.9551 (m-10) cc_final: 0.9170 (m-10) REVERT: A 450 TYR cc_start: 0.9092 (p90) cc_final: 0.8615 (p90) REVERT: A 495 MET cc_start: 0.9479 (mmp) cc_final: 0.8905 (tpt) REVERT: A 587 PHE cc_start: 0.9507 (m-10) cc_final: 0.9127 (m-80) REVERT: A 694 MET cc_start: 0.9230 (tpt) cc_final: 0.9010 (tpp) REVERT: A 1089 MET cc_start: 0.7321 (tpp) cc_final: 0.6991 (tpp) REVERT: A 1099 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9288 (mp0) REVERT: A 1204 PHE cc_start: 0.9823 (m-80) cc_final: 0.9413 (m-80) REVERT: A 1213 MET cc_start: 0.9755 (tpt) cc_final: 0.9399 (tmm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1000 time to fit residues: 12.7225 Evaluate side-chains 66 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 50.0000 chunk 84 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 71 optimal weight: 40.0000 overall best weight: 11.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** 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 = 0.3054 r_free = 0.3054 target = 0.038802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.027687 restraints weight = 146219.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.028696 restraints weight = 92099.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.029400 restraints weight = 68072.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.029882 restraints weight = 55215.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.030164 restraints weight = 47664.852| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 12013 Z= 0.305 Angle : 0.796 10.544 16879 Z= 0.438 Chirality : 0.047 0.250 1953 Planarity : 0.006 0.094 1596 Dihedral : 19.883 154.816 3169 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -0.25 (0.25), residues: 1006 helix: 0.19 (0.22), residues: 520 sheet: 0.42 (0.66), residues: 60 loop : -0.55 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.033 0.003 TYR A 128 PHE 0.032 0.003 PHE A 119 TRP 0.020 0.003 TRP A 659 HIS 0.016 0.003 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.31 (12013) covalent geometry : angle 0.79624 / 0.44 (16879) hydrogen bonds : bond 0.09751 / 6.58 ( 532) hydrogen bonds : angle 5.04127 / 3.57 ( 1414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.251 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 86 PHE cc_start: 0.9638 (m-10) cc_final: 0.9434 (m-80) REVERT: A 90 MET cc_start: 0.9041 (ppp) cc_final: 0.8563 (ttp) REVERT: A 161 MET cc_start: 0.9821 (ttt) cc_final: 0.9378 (tpp) REVERT: A 450 TYR cc_start: 0.8817 (p90) cc_final: 0.8582 (p90) REVERT: A 495 MET cc_start: 0.9005 (mmp) cc_final: 0.8475 (tpt) REVERT: A 501 ASN cc_start: 0.8388 (p0) cc_final: 0.8113 (p0) REVERT: A 587 PHE cc_start: 0.9377 (m-10) cc_final: 0.8974 (m-80) REVERT: A 1089 MET cc_start: 0.7277 (tpp) cc_final: 0.6910 (tpp) REVERT: A 1099 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9216 (mp0) REVERT: A 1204 PHE cc_start: 0.9747 (m-80) cc_final: 0.9410 (m-80) REVERT: A 1213 MET cc_start: 0.9720 (tpt) cc_final: 0.9501 (tmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0941 time to fit residues: 10.0542 Evaluate side-chains 57 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 16 optimal weight: 8.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS A 489 GLN A 497 ASN A 739 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.050958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.042330 restraints weight = 152144.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.043479 restraints weight = 85860.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.044228 restraints weight = 58747.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.044730 restraints weight = 44952.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.045038 restraints weight = 37184.258| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12013 Z= 0.160 Angle : 0.583 6.916 16879 Z= 0.338 Chirality : 0.042 0.237 1953 Planarity : 0.004 0.050 1596 Dihedral : 19.858 154.478 3169 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: 0.21 (0.26), residues: 1006 helix: 0.60 (0.22), residues: 514 sheet: 1.19 (0.60), residues: 69 loop : -0.52 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 63 TYR 0.016 0.002 TYR A 128 PHE 0.027 0.002 PHE A 693 TRP 0.013 0.002 TRP A 476 HIS 0.015 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (12013) covalent geometry : angle 0.58251 / 0.34 (16879) hydrogen bonds : bond 0.04984 / 3.46 ( 532) hydrogen bonds : angle 4.61760 / 3.26 ( 1414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.234 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 82 LEU cc_start: 0.9737 (tp) cc_final: 0.9111 (tt) REVERT: A 161 MET cc_start: 0.9665 (ttt) cc_final: 0.9025 (tpp) REVERT: A 163 LYS cc_start: 0.9166 (pttm) cc_final: 0.8730 (pttp) REVERT: A 450 TYR cc_start: 0.9376 (p90) cc_final: 0.9025 (p90) REVERT: A 587 PHE cc_start: 0.9445 (m-10) cc_final: 0.9051 (m-80) REVERT: A 694 MET cc_start: 0.9419 (tpt) cc_final: 0.9181 (tpp) REVERT: A 986 ASP cc_start: 0.9735 (t0) cc_final: 0.9532 (m-30) REVERT: A 1089 MET cc_start: 0.7469 (tpp) cc_final: 0.6658 (tpp) REVERT: A 1164 LEU cc_start: 0.9302 (mt) cc_final: 0.9083 (mt) REVERT: A 1204 PHE cc_start: 0.9724 (m-80) cc_final: 0.9142 (m-80) REVERT: A 1213 MET cc_start: 0.9651 (tpp) cc_final: 0.9341 (tmm) REVERT: A 1317 ASN cc_start: 0.8983 (m110) cc_final: 0.8709 (m110) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1019 time to fit residues: 10.5029 Evaluate side-chains 56 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 0.0010 chunk 45 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 102 optimal weight: 50.0000 chunk 48 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 114 optimal weight: 50.0000 overall best weight: 5.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 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 = 0.3289 r_free = 0.3289 target = 0.050273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041724 restraints weight = 152035.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.042861 restraints weight = 86136.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.043609 restraints weight = 59114.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.044084 restraints weight = 45410.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.044443 restraints weight = 37859.353| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12013 Z= 0.165 Angle : 0.553 6.721 16879 Z= 0.324 Chirality : 0.040 0.239 1953 Planarity : 0.004 0.047 1596 Dihedral : 19.846 153.045 3169 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 0.38 (0.26), residues: 1006 helix: 0.79 (0.22), residues: 517 sheet: 1.27 (0.59), residues: 69 loop : -0.51 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.010 0.001 TYR A1242 PHE 0.017 0.002 PHE A 86 TRP 0.007 0.002 TRP A 476 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (12013) covalent geometry : angle 0.55337 / 0.32 (16879) hydrogen bonds : bond 0.05077 / 3.46 ( 532) hydrogen bonds : angle 4.50533 / 3.18 ( 1414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.305 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 82 LEU cc_start: 0.9610 (tp) cc_final: 0.9325 (tt) REVERT: A 86 PHE cc_start: 0.9170 (m-80) cc_final: 0.8930 (m-80) REVERT: A 161 MET cc_start: 0.9702 (ttt) cc_final: 0.9066 (tpp) REVERT: A 163 LYS cc_start: 0.9060 (pttm) cc_final: 0.8340 (pttp) REVERT: A 164 PHE cc_start: 0.9410 (m-80) cc_final: 0.8973 (m-80) REVERT: A 450 TYR cc_start: 0.9395 (p90) cc_final: 0.9113 (p90) REVERT: A 587 PHE cc_start: 0.9418 (m-10) cc_final: 0.9020 (m-80) REVERT: A 694 MET cc_start: 0.9421 (tpt) cc_final: 0.9196 (tpp) REVERT: A 986 ASP cc_start: 0.9735 (t0) cc_final: 0.9532 (m-30) REVERT: A 1089 MET cc_start: 0.7459 (tpp) cc_final: 0.6635 (tpp) REVERT: A 1164 LEU cc_start: 0.9296 (mt) cc_final: 0.9080 (mt) REVERT: A 1171 ARG cc_start: 0.9495 (ppt170) cc_final: 0.9213 (ttp80) REVERT: A 1204 PHE cc_start: 0.9731 (m-80) cc_final: 0.9155 (m-80) REVERT: A 1317 ASN cc_start: 0.9024 (m110) cc_final: 0.8758 (m110) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1069 time to fit residues: 11.1141 Evaluate side-chains 59 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 103 optimal weight: 40.0000 chunk 42 optimal weight: 40.0000 chunk 72 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 110 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A 754 HIS ** A 983 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 = 0.3107 r_free = 0.3107 target = 0.041142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.029459 restraints weight = 142380.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.030469 restraints weight = 93154.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.031159 restraints weight = 69938.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.031641 restraints weight = 57336.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.031962 restraints weight = 49791.517| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12013 Z= 0.224 Angle : 0.632 7.460 16879 Z= 0.365 Chirality : 0.042 0.230 1953 Planarity : 0.005 0.071 1596 Dihedral : 19.977 149.863 3169 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 0.03 (0.26), residues: 1006 helix: 0.47 (0.22), residues: 515 sheet: 0.84 (0.59), residues: 72 loop : -0.57 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 535 TYR 0.014 0.002 TYR A 515 PHE 0.021 0.002 PHE A 98 TRP 0.009 0.002 TRP A 659 HIS 0.010 0.002 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.22 (12013) covalent geometry : angle 0.63183 / 0.36 (16879) hydrogen bonds : bond 0.06527 / 4.43 ( 532) hydrogen bonds : angle 4.67065 / 3.30 ( 1414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.9387 (m-80) cc_final: 0.9066 (m-80) REVERT: A 161 MET cc_start: 0.9724 (ttt) cc_final: 0.9360 (tpp) REVERT: A 163 LYS cc_start: 0.8887 (pttm) cc_final: 0.8599 (pttp) REVERT: A 164 PHE cc_start: 0.9293 (m-80) cc_final: 0.9090 (m-80) REVERT: A 587 PHE cc_start: 0.8916 (m-10) cc_final: 0.8545 (m-80) REVERT: A 1089 MET cc_start: 0.5932 (tpp) cc_final: 0.5580 (tpp) REVERT: A 1204 PHE cc_start: 0.9601 (m-80) cc_final: 0.9307 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0884 time to fit residues: 8.9992 Evaluate side-chains 53 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 112 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 97 optimal weight: 0.4980 chunk 79 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 110 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 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 = 0.3261 r_free = 0.3261 target = 0.049043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.040505 restraints weight = 150844.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.041576 restraints weight = 86054.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.042287 restraints weight = 59680.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.042741 restraints weight = 46127.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.043095 restraints weight = 38766.114| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12013 Z= 0.170 Angle : 0.585 9.211 16879 Z= 0.338 Chirality : 0.042 0.233 1953 Planarity : 0.004 0.044 1596 Dihedral : 19.955 148.501 3169 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1006 helix: 0.56 (0.22), residues: 514 sheet: 1.11 (0.61), residues: 70 loop : -0.54 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.026 0.002 TYR A 81 PHE 0.020 0.002 PHE A 98 TRP 0.005 0.002 TRP A 659 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (12013) covalent geometry : angle 0.58547 / 0.34 (16879) hydrogen bonds : bond 0.04935 / 3.39 ( 532) hydrogen bonds : angle 4.57109 / 3.23 ( 1414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.9224 (m-80) cc_final: 0.8838 (t80) REVERT: A 90 MET cc_start: 0.8544 (ttt) cc_final: 0.7574 (ttt) REVERT: A 161 MET cc_start: 0.9713 (ttt) cc_final: 0.9072 (tpp) REVERT: A 163 LYS cc_start: 0.8962 (pttm) cc_final: 0.8350 (pttp) REVERT: A 164 PHE cc_start: 0.9347 (m-80) cc_final: 0.9012 (m-80) REVERT: A 587 PHE cc_start: 0.9437 (m-10) cc_final: 0.9020 (m-80) REVERT: A 1164 LEU cc_start: 0.9261 (mt) cc_final: 0.9053 (mt) REVERT: A 1171 ARG cc_start: 0.9511 (ppt170) cc_final: 0.9252 (ttp80) REVERT: A 1204 PHE cc_start: 0.9712 (m-80) cc_final: 0.9171 (m-80) REVERT: A 1317 ASN cc_start: 0.9012 (m110) cc_final: 0.8753 (m110) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0931 time to fit residues: 9.1772 Evaluate side-chains 52 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 50.0000 chunk 4 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 overall best weight: 5.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 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 = 0.3251 r_free = 0.3251 target = 0.048590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.040115 restraints weight = 153718.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.041189 restraints weight = 87152.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.041852 restraints weight = 60376.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.042349 restraints weight = 47195.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.042688 restraints weight = 39341.591| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12013 Z= 0.175 Angle : 0.576 8.874 16879 Z= 0.334 Chirality : 0.041 0.235 1953 Planarity : 0.004 0.045 1596 Dihedral : 19.947 146.324 3169 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.88 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1006 helix: 0.47 (0.22), residues: 520 sheet: 1.11 (0.62), residues: 69 loop : -0.64 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.022 0.002 TYR A 81 PHE 0.038 0.002 PHE A 693 TRP 0.008 0.002 TRP A 659 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (12013) covalent geometry : angle 0.57626 / 0.33 (16879) hydrogen bonds : bond 0.05134 / 3.50 ( 532) hydrogen bonds : angle 4.51802 / 3.20 ( 1414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9683 (ttt) cc_final: 0.9008 (tpp) REVERT: A 163 LYS cc_start: 0.8943 (pttm) cc_final: 0.8443 (pttp) REVERT: A 164 PHE cc_start: 0.9315 (m-80) cc_final: 0.9062 (m-80) REVERT: A 587 PHE cc_start: 0.9445 (m-10) cc_final: 0.9047 (m-80) REVERT: A 1164 LEU cc_start: 0.9245 (mt) cc_final: 0.9038 (mt) REVERT: A 1171 ARG cc_start: 0.9523 (ppt170) cc_final: 0.9260 (ttp80) REVERT: A 1204 PHE cc_start: 0.9722 (m-80) cc_final: 0.9205 (m-80) REVERT: A 1317 ASN cc_start: 0.8985 (m110) cc_final: 0.8739 (m110) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0857 time to fit residues: 8.4576 Evaluate side-chains 52 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 104 optimal weight: 50.0000 chunk 100 optimal weight: 40.0000 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 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 = 0.3262 r_free = 0.3262 target = 0.049027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.040649 restraints weight = 153505.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.041728 restraints weight = 85340.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.042431 restraints weight = 58790.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.042918 restraints weight = 45502.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.043229 restraints weight = 37734.022| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12013 Z= 0.146 Angle : 0.554 8.071 16879 Z= 0.320 Chirality : 0.040 0.238 1953 Planarity : 0.004 0.043 1596 Dihedral : 19.894 145.549 3169 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.15 (0.26), residues: 1006 helix: 0.53 (0.22), residues: 522 sheet: 1.30 (0.63), residues: 70 loop : -0.56 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.026 0.001 TYR A 81 PHE 0.024 0.002 PHE A 693 TRP 0.006 0.001 TRP A 659 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (12013) covalent geometry : angle 0.55409 / 0.32 (16879) hydrogen bonds : bond 0.04337 / 2.97 ( 532) hydrogen bonds : angle 4.46891 / 3.16 ( 1414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1460.28 seconds wall clock time: 26 minutes 11.94 seconds (1571.94 seconds total)