Starting phenix.real_space_refine on Thu Aug 6 03:40:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6o_41073/08_2026/8t6o_41073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6o_41073/08_2026/8t6o_41073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6o_41073/08_2026/8t6o_41073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6o_41073/08_2026/8t6o_41073.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6o_41073/08_2026/8t6o_41073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6o_41073/08_2026/8t6o_41073.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1668 atoms to isotropic. 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 130 5.49 5 S 19 5.16 5 C 7106 2.51 5 N 2080 2.21 5 O 2569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 11904 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 9151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 9151 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 32, 'TRANS': 1104} Chain breaks: 3 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 5, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1854 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 41, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 74} Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 443 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Time building chain proxies: 2.63, per 1000 atoms: 0.22 Number of scatterers: 11904 At special positions: 0 Unit cell: (88.3192, 123.314, 122.48, 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 19 16.00 P 130 15.00 O 2569 8.00 N 2080 7.00 C 7106 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: 1.00 Conformation dependent library (CDL) restraints added in 589.0 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 56.6% alpha, 8.8% beta 41 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.085A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.819A 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 175 through 180 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.510A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.028A pdb=" N GLY A 205 " --> pdb=" O ASN A 202 " (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 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.631A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 306 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 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 removed outlier: 3.552A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.558A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.918A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.724A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.800A pdb=" N VAL A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.532A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 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 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.522A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.567A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.538A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 removed outlier: 3.854A pdb=" N HIS A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.692A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 removed outlier: 3.564A pdb=" N ILE A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.699A pdb=" N TYR A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 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: 3.594A pdb=" N PHE A1258 " --> pdb=" O GLN A1254 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A1259 " --> pdb=" O LYS A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 4.758A pdb=" N ILE A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1311 Processing helix chain 'A' and resid 1312 through 1315 Processing helix chain 'A' and resid 1339 through 1343 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 4.599A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.052A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A1346 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.934A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.614A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.472A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A1109 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1157 through 1167 Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.966A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.30: 1680 1.30 - 1.53: 9548 1.53 - 1.76: 1134 1.76 - 1.99: 36 1.99 - 2.21: 1 Bond restraints: 12399 Sorted by residual: bond pdb=" CB PRO A 731 " pdb=" CG PRO A 731 " ideal model delta sigma weight residual 1.492 2.214 -0.722 5.00e-02 4.00e+02 2.09e+02 bond pdb=" CG PRO A 731 " pdb=" CD PRO A 731 " ideal model delta sigma weight residual 1.503 1.073 0.430 3.40e-02 8.65e+02 1.60e+02 bond pdb=" C5' DG D 16 " pdb=" C4' DG D 16 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.54e+01 bond pdb=" C1' DT D 26 " pdb=" N1 DT D 26 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.54e+01 bond pdb=" C3' DG C 13 " pdb=" O3' DG C 13 " ideal model delta sigma weight residual 1.435 1.498 -0.063 1.30e-02 5.92e+03 2.31e+01 ... (remaining 12394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.37: 17320 14.37 - 28.74: 3 28.74 - 43.11: 1 43.11 - 57.48: 0 57.48 - 71.85: 1 Bond angle restraints: 17325 Sorted by residual: angle pdb=" CA PRO A 731 " pdb=" N PRO A 731 " pdb=" CD PRO A 731 " ideal model delta sigma weight residual 112.00 77.83 34.17 1.40e+00 5.10e-01 5.96e+02 angle pdb=" CB PRO A 731 " pdb=" CG PRO A 731 " pdb=" CD PRO A 731 " ideal model delta sigma weight residual 106.10 34.25 71.85 3.20e+00 9.77e-02 5.04e+02 angle pdb=" N PRO A 731 " pdb=" CD PRO A 731 " pdb=" CG PRO A 731 " ideal model delta sigma weight residual 103.20 118.98 -15.78 1.50e+00 4.44e-01 1.11e+02 angle pdb=" N PRO A 731 " pdb=" CA PRO A 731 " pdb=" CB PRO A 731 " ideal model delta sigma weight residual 103.25 93.31 9.94 1.05e+00 9.07e-01 8.96e+01 angle pdb=" O4' DG C 11 " pdb=" C4' DG C 11 " pdb=" C3' DG C 11 " ideal model delta sigma weight residual 106.00 101.76 4.24 6.00e-01 2.78e+00 4.99e+01 ... (remaining 17320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.00: 6874 29.00 - 58.00: 512 58.00 - 87.00: 119 87.00 - 116.00: 8 116.00 - 145.00: 2 Dihedral angle restraints: 7515 sinusoidal: 4171 harmonic: 3344 Sorted by residual: dihedral pdb=" N PRO A 731 " pdb=" CG PRO A 731 " pdb=" CD PRO A 731 " pdb=" CB PRO A 731 " ideal model delta sinusoidal sigma weight residual 30.00 117.77 -87.77 1 1.50e+01 4.44e-03 4.10e+01 dihedral pdb=" CA LEU A1266 " pdb=" C LEU A1266 " pdb=" N ASP A1267 " pdb=" CA ASP A1267 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLU A1271 " pdb=" C GLU A1271 " pdb=" N GLN A1272 " pdb=" CA GLN A1272 " ideal model delta harmonic sigma weight residual 180.00 156.79 23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1516 0.066 - 0.133: 412 0.133 - 0.199: 71 0.199 - 0.265: 6 0.265 - 0.331: 4 Chirality restraints: 2009 Sorted by residual: chirality pdb=" CA PRO A 731 " pdb=" N PRO A 731 " pdb=" C PRO A 731 " pdb=" CB PRO A 731 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C3' DG C 11 " pdb=" C4' DG C 11 " pdb=" O3' DG C 11 " pdb=" C2' DG C 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2006 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 730 " -0.098 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO A 731 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 645 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" CG ASP A 645 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASP A 645 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP A 645 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 25 " 0.049 2.00e-02 2.50e+03 1.97e-02 1.16e+01 pdb=" N9 DG D 25 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG D 25 " -0.017 2.00e-02 2.50e+03 pdb=" N7 DG D 25 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG D 25 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG D 25 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG D 25 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DG D 25 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG D 25 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG D 25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG D 25 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG D 25 " -0.009 2.00e-02 2.50e+03 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1367 2.75 - 3.29: 11611 3.29 - 3.83: 21331 3.83 - 4.36: 25091 4.36 - 4.90: 39284 Nonbonded interactions: 98684 Sorted by model distance: nonbonded pdb=" OG1 THR A 525 " pdb=" OD1 ASN A 690 " model vdw 2.217 3.040 nonbonded pdb=" O LEU A1266 " pdb=" OH TYR A1294 " model vdw 2.229 3.040 nonbonded pdb=" O TYR A1237 " pdb=" OG SER A1240 " model vdw 2.301 3.040 nonbonded pdb=" O LEU A1291 " pdb=" ND2 ASN A1295 " model vdw 2.313 3.120 nonbonded pdb=" OD1 ASN A 609 " pdb=" OE1 GLU A 611 " model vdw 2.328 3.040 ... (remaining 98679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.340 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.009 0.722 12399 Z= 0.417 Angle : 1.279 71.848 17325 Z= 0.791 Chirality : 0.062 0.331 2009 Planarity : 0.006 0.123 1736 Dihedral : 19.518 145.001 5347 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.41 % Allowed : 13.53 % Favored : 86.06 % Cbeta Deviations : 0.09 % 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: -1.13 (0.23), residues: 1129 helix: -0.76 (0.19), residues: 574 sheet: -0.19 (0.43), residues: 118 loop : -0.63 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1114 TYR 0.030 0.003 TYR A 25 PHE 0.035 0.003 PHE A1046 TRP 0.029 0.003 TRP A1136 HIS 0.013 0.002 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00945 / 0.42 (12399) covalent geometry : angle 1.27883 / 0.79 (17325) hydrogen bonds : bond 0.16116 / 17.90 ( 554) hydrogen bonds : angle 7.06848 / 7.26 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.332 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 251 ASN cc_start: 0.8769 (m-40) cc_final: 0.7678 (m-40) REVERT: A 263 LYS cc_start: 0.9397 (tttp) cc_final: 0.8993 (mmtt) REVERT: A 304 ASP cc_start: 0.8845 (m-30) cc_final: 0.8608 (m-30) REVERT: A 370 GLU cc_start: 0.7919 (tt0) cc_final: 0.7226 (tm-30) REVERT: A 696 LEU cc_start: 0.8438 (mt) cc_final: 0.8226 (mt) REVERT: A 1189 GLU cc_start: 0.8699 (tp30) cc_final: 0.8351 (tp30) REVERT: A 1312 LEU cc_start: 0.8925 (tp) cc_final: 0.8655 (mt) outliers start: 4 outliers final: 0 residues processed: 133 average time/residue: 0.1069 time to fit residues: 21.1326 Evaluate side-chains 104 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.109800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076889 restraints weight = 33666.563| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.30 r_work: 0.3258 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 12399 Z= 0.174 Angle : 0.687 8.312 17325 Z= 0.384 Chirality : 0.046 0.348 2009 Planarity : 0.005 0.064 1736 Dihedral : 20.851 141.214 3042 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.73 % Allowed : 10.78 % Favored : 87.49 % 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: -0.33 (0.24), residues: 1129 helix: 0.17 (0.21), residues: 577 sheet: -0.39 (0.43), residues: 119 loop : -0.49 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 494 TYR 0.020 0.002 TYR A1294 PHE 0.034 0.002 PHE A1313 TRP 0.013 0.002 TRP A1136 HIS 0.004 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (12399) covalent geometry : angle 0.68716 / 0.38 (17325) hydrogen bonds : bond 0.05836 / 6.36 ( 554) hydrogen bonds : angle 5.44314 / 5.76 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8738 (tp30) cc_final: 0.8410 (tp30) REVERT: A 251 ASN cc_start: 0.9163 (m-40) cc_final: 0.8534 (m-40) REVERT: A 263 LYS cc_start: 0.9432 (tttp) cc_final: 0.9105 (mmtt) REVERT: A 370 GLU cc_start: 0.8227 (tt0) cc_final: 0.7600 (tm-30) REVERT: A 502 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 696 LEU cc_start: 0.8217 (mt) cc_final: 0.7973 (mt) REVERT: A 763 MET cc_start: 0.9039 (tpp) cc_final: 0.8327 (mtp) REVERT: A 1356 TYR cc_start: 0.8668 (m-10) cc_final: 0.8401 (m-80) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 0.0869 time to fit residues: 15.5706 Evaluate side-chains 102 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 87 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 990 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 = 0.3975 r_free = 0.3975 target = 0.106093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073212 restraints weight = 34230.594| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.29 r_work: 0.3152 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 12399 Z= 0.269 Angle : 0.717 8.815 17325 Z= 0.390 Chirality : 0.046 0.313 2009 Planarity : 0.004 0.051 1736 Dihedral : 20.884 142.275 3042 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.05 % Allowed : 11.09 % Favored : 85.86 % 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: -0.18 (0.24), residues: 1129 helix: 0.44 (0.21), residues: 583 sheet: -0.40 (0.45), residues: 119 loop : -0.66 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1210 TYR 0.027 0.002 TYR A 362 PHE 0.016 0.002 PHE A 252 TRP 0.008 0.002 TRP A1074 HIS 0.016 0.002 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.27 (12399) covalent geometry : angle 0.71673 / 0.39 (17325) hydrogen bonds : bond 0.05782 / 6.35 ( 554) hydrogen bonds : angle 5.32657 / 5.61 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8850 (tp30) cc_final: 0.8644 (tp30) REVERT: A 251 ASN cc_start: 0.9226 (m-40) cc_final: 0.8301 (m-40) REVERT: A 263 LYS cc_start: 0.9458 (tttp) cc_final: 0.9060 (mmtt) REVERT: A 524 LEU cc_start: 0.8577 (pp) cc_final: 0.8291 (mm) REVERT: A 560 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.6983 (t) REVERT: A 670 ILE cc_start: 0.8023 (mm) cc_final: 0.7781 (mp) REVERT: A 763 MET cc_start: 0.9017 (tpp) cc_final: 0.8359 (mtp) REVERT: A 1180 ASP cc_start: 0.9123 (t0) cc_final: 0.8894 (t0) outliers start: 30 outliers final: 15 residues processed: 119 average time/residue: 0.0902 time to fit residues: 16.5165 Evaluate side-chains 103 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1305 GLN Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A 726 ASN A 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.107190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073838 restraints weight = 33949.484| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.31 r_work: 0.3205 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12399 Z= 0.137 Angle : 0.603 8.969 17325 Z= 0.332 Chirality : 0.042 0.296 2009 Planarity : 0.004 0.050 1736 Dihedral : 20.891 141.497 3042 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.03 % Allowed : 13.22 % Favored : 84.74 % 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: 0.18 (0.25), residues: 1129 helix: 0.80 (0.22), residues: 578 sheet: -0.42 (0.45), residues: 120 loop : -0.52 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 400 TYR 0.017 0.001 TYR A 362 PHE 0.011 0.001 PHE A 491 TRP 0.008 0.001 TRP A1136 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (12399) covalent geometry : angle 0.60252 / 0.33 (17325) hydrogen bonds : bond 0.04659 / 5.24 ( 554) hydrogen bonds : angle 4.99271 / 5.27 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8774 (tp30) cc_final: 0.8462 (tp30) REVERT: A 110 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.7992 (p0) REVERT: A 251 ASN cc_start: 0.9188 (m-40) cc_final: 0.8319 (m-40) REVERT: A 263 LYS cc_start: 0.9466 (tttp) cc_final: 0.9076 (mmtt) REVERT: A 524 LEU cc_start: 0.8820 (pp) cc_final: 0.8443 (mm) REVERT: A 544 GLN cc_start: 0.9266 (mt0) cc_final: 0.8913 (pt0) REVERT: A 627 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 631 MET cc_start: 0.8814 (tpp) cc_final: 0.8563 (tpp) REVERT: A 763 MET cc_start: 0.9010 (tpp) cc_final: 0.8397 (mtp) REVERT: A 1043 MET cc_start: 0.7944 (pmm) cc_final: 0.6709 (tmm) REVERT: A 1180 ASP cc_start: 0.9040 (t0) cc_final: 0.8807 (t0) REVERT: A 1189 GLU cc_start: 0.8988 (tp30) cc_final: 0.8648 (tp30) REVERT: A 1312 LEU cc_start: 0.9152 (mt) cc_final: 0.8759 (mt) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 0.0853 time to fit residues: 14.9616 Evaluate side-chains 107 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 40.0000 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.106495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073418 restraints weight = 34183.223| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.26 r_work: 0.3194 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12399 Z= 0.149 Angle : 0.589 8.257 17325 Z= 0.323 Chirality : 0.042 0.291 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.834 142.902 3042 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.24 % Allowed : 12.51 % Favored : 85.25 % 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: 0.29 (0.25), residues: 1129 helix: 0.91 (0.22), residues: 586 sheet: -0.40 (0.46), residues: 119 loop : -0.51 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 967 TYR 0.018 0.001 TYR A1201 PHE 0.011 0.001 PHE A1258 TRP 0.007 0.001 TRP A1136 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (12399) covalent geometry : angle 0.58900 / 0.32 (17325) hydrogen bonds : bond 0.04494 / 5.03 ( 554) hydrogen bonds : angle 4.94955 / 5.27 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8759 (tp30) cc_final: 0.8420 (tp30) REVERT: A 251 ASN cc_start: 0.9167 (m-40) cc_final: 0.8077 (m-40) REVERT: A 263 LYS cc_start: 0.9501 (tttp) cc_final: 0.9085 (mmtt) REVERT: A 304 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8494 (m-30) REVERT: A 524 LEU cc_start: 0.8781 (pp) cc_final: 0.8442 (mm) REVERT: A 544 GLN cc_start: 0.9263 (mt0) cc_final: 0.8939 (pt0) REVERT: A 627 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 631 MET cc_start: 0.8826 (tpp) cc_final: 0.8559 (tpp) REVERT: A 746 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: A 1043 MET cc_start: 0.7990 (pmm) cc_final: 0.6770 (tmm) REVERT: A 1180 ASP cc_start: 0.9042 (t0) cc_final: 0.8820 (t0) REVERT: A 1189 GLU cc_start: 0.9003 (tp30) cc_final: 0.8673 (tp30) REVERT: A 1312 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8796 (mt) outliers start: 22 outliers final: 12 residues processed: 112 average time/residue: 0.0748 time to fit residues: 13.1703 Evaluate side-chains 105 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.106826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073634 restraints weight = 34267.822| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.30 r_work: 0.3205 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12399 Z= 0.130 Angle : 0.581 9.845 17325 Z= 0.315 Chirality : 0.041 0.290 2009 Planarity : 0.003 0.055 1736 Dihedral : 20.818 143.367 3042 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.64 % Allowed : 12.72 % Favored : 84.64 % 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 (0.25), residues: 1129 helix: 0.97 (0.22), residues: 587 sheet: -0.37 (0.46), residues: 120 loop : -0.43 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 557 TYR 0.015 0.001 TYR A 362 PHE 0.011 0.001 PHE A 966 TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (12399) covalent geometry : angle 0.58062 / 0.31 (17325) hydrogen bonds : bond 0.04266 / 4.82 ( 554) hydrogen bonds : angle 4.86618 / 5.16 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 60 GLU cc_start: 0.8746 (tp30) cc_final: 0.8393 (tp30) REVERT: A 110 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7635 (p0) REVERT: A 251 ASN cc_start: 0.9153 (m-40) cc_final: 0.8780 (m-40) REVERT: A 304 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8492 (m-30) REVERT: A 524 LEU cc_start: 0.8786 (pp) cc_final: 0.8421 (mm) REVERT: A 627 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 631 MET cc_start: 0.8831 (tpp) cc_final: 0.8551 (tpp) REVERT: A 746 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: A 763 MET cc_start: 0.9009 (tpp) cc_final: 0.8321 (mtp) REVERT: A 1043 MET cc_start: 0.7981 (pmm) cc_final: 0.6782 (tmm) REVERT: A 1180 ASP cc_start: 0.9047 (t0) cc_final: 0.8825 (t0) REVERT: A 1189 GLU cc_start: 0.9011 (tp30) cc_final: 0.8687 (tp30) REVERT: A 1312 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8760 (mt) outliers start: 26 outliers final: 13 residues processed: 111 average time/residue: 0.0877 time to fit residues: 14.9164 Evaluate side-chains 100 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.106749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073555 restraints weight = 33994.601| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.27 r_work: 0.3208 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12399 Z= 0.128 Angle : 0.578 10.154 17325 Z= 0.313 Chirality : 0.040 0.288 2009 Planarity : 0.004 0.050 1736 Dihedral : 20.784 144.101 3042 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 2.85 % Allowed : 12.92 % Favored : 84.23 % 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: 0.49 (0.25), residues: 1129 helix: 1.08 (0.22), residues: 589 sheet: -0.32 (0.47), residues: 117 loop : -0.44 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 215 TYR 0.019 0.001 TYR A1201 PHE 0.017 0.001 PHE A1258 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (12399) covalent geometry : angle 0.57775 / 0.31 (17325) hydrogen bonds : bond 0.04114 / 4.64 ( 554) hydrogen bonds : angle 4.80244 / 5.09 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7916 (tt) REVERT: A 60 GLU cc_start: 0.8726 (tp30) cc_final: 0.8365 (tp30) REVERT: A 110 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7617 (p0) REVERT: A 524 LEU cc_start: 0.8781 (pp) cc_final: 0.8398 (mm) REVERT: A 627 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 631 MET cc_start: 0.8851 (tpp) cc_final: 0.8569 (tpp) REVERT: A 746 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: A 1043 MET cc_start: 0.8028 (pmm) cc_final: 0.6885 (tmm) REVERT: A 1180 ASP cc_start: 0.9028 (t0) cc_final: 0.8799 (t0) REVERT: A 1189 GLU cc_start: 0.9036 (tp30) cc_final: 0.8731 (tp30) REVERT: A 1241 HIS cc_start: 0.8475 (m90) cc_final: 0.8060 (m90) REVERT: A 1312 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8794 (mt) outliers start: 28 outliers final: 14 residues processed: 106 average time/residue: 0.0664 time to fit residues: 11.3615 Evaluate side-chains 98 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.106880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.073877 restraints weight = 34062.771| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.25 r_work: 0.3216 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12399 Z= 0.126 Angle : 0.575 10.560 17325 Z= 0.307 Chirality : 0.040 0.286 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.734 145.084 3042 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.85 % Allowed : 13.02 % Favored : 84.13 % 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: 0.56 (0.25), residues: 1129 helix: 1.14 (0.22), residues: 589 sheet: -0.30 (0.49), residues: 109 loop : -0.42 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 967 TYR 0.014 0.001 TYR A 362 PHE 0.012 0.001 PHE A 966 TRP 0.009 0.001 TRP A 464 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (12399) covalent geometry : angle 0.57466 / 0.31 (17325) hydrogen bonds : bond 0.03965 / 4.48 ( 554) hydrogen bonds : angle 4.73693 / 5.00 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8116 (tt) REVERT: A 60 GLU cc_start: 0.8700 (tp30) cc_final: 0.8325 (tp30) REVERT: A 110 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7623 (p0) REVERT: A 304 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: A 627 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 631 MET cc_start: 0.8869 (tpp) cc_final: 0.8600 (tpp) REVERT: A 746 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: A 763 MET cc_start: 0.8948 (tpp) cc_final: 0.8638 (ttt) REVERT: A 1043 MET cc_start: 0.8034 (pmm) cc_final: 0.6892 (tmm) REVERT: A 1180 ASP cc_start: 0.9002 (t0) cc_final: 0.8760 (t0) REVERT: A 1189 GLU cc_start: 0.9061 (tp30) cc_final: 0.8769 (tp30) REVERT: A 1312 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8802 (mt) outliers start: 28 outliers final: 16 residues processed: 103 average time/residue: 0.0720 time to fit residues: 12.0017 Evaluate side-chains 102 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 106 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 116 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN A 255 ASN A 726 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.106435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.073386 restraints weight = 34157.953| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.25 r_work: 0.3205 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12399 Z= 0.137 Angle : 0.574 10.838 17325 Z= 0.306 Chirality : 0.040 0.282 2009 Planarity : 0.003 0.050 1736 Dihedral : 20.705 145.586 3042 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 2.75 % Allowed : 13.43 % Favored : 83.83 % 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 (0.25), residues: 1129 helix: 1.17 (0.22), residues: 583 sheet: -0.23 (0.50), residues: 109 loop : -0.37 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 494 TYR 0.015 0.001 TYR A1201 PHE 0.012 0.001 PHE A 966 TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (12399) covalent geometry : angle 0.57371 / 0.31 (17325) hydrogen bonds : bond 0.04024 / 4.53 ( 554) hydrogen bonds : angle 4.74867 / 4.99 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8088 (tt) REVERT: A 60 GLU cc_start: 0.8725 (tp30) cc_final: 0.8355 (tp30) REVERT: A 110 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7659 (p0) REVERT: A 304 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: A 524 LEU cc_start: 0.8557 (pp) cc_final: 0.8201 (mm) REVERT: A 627 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 631 MET cc_start: 0.8863 (tpp) cc_final: 0.8585 (tpp) REVERT: A 746 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: A 763 MET cc_start: 0.8966 (tpp) cc_final: 0.8723 (ttt) REVERT: A 1043 MET cc_start: 0.8059 (pmm) cc_final: 0.6929 (tmm) REVERT: A 1180 ASP cc_start: 0.9026 (t0) cc_final: 0.8800 (t0) REVERT: A 1189 GLU cc_start: 0.9101 (tp30) cc_final: 0.8805 (tp30) REVERT: A 1312 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8793 (mt) outliers start: 27 outliers final: 18 residues processed: 102 average time/residue: 0.0928 time to fit residues: 14.7690 Evaluate side-chains 103 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 77 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.0170 chunk 80 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.107020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074063 restraints weight = 34417.689| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.26 r_work: 0.3223 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12399 Z= 0.116 Angle : 0.572 11.511 17325 Z= 0.302 Chirality : 0.039 0.277 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.683 145.895 3042 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 1.93 % Allowed : 14.75 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1129 helix: 1.14 (0.22), residues: 588 sheet: -0.10 (0.52), residues: 109 loop : -0.34 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.016 0.001 TYR A 568 PHE 0.012 0.001 PHE A 966 TRP 0.005 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (12399) covalent geometry : angle 0.57198 / 0.30 (17325) hydrogen bonds : bond 0.03891 / 4.38 ( 554) hydrogen bonds : angle 4.68998 / 4.93 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7524 (p90) cc_final: 0.7080 (p90) REVERT: A 51 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8079 (tt) REVERT: A 60 GLU cc_start: 0.8665 (tp30) cc_final: 0.8291 (tp30) REVERT: A 304 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: A 524 LEU cc_start: 0.8623 (pp) cc_final: 0.8228 (mm) REVERT: A 627 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 631 MET cc_start: 0.8862 (tpp) cc_final: 0.8593 (tpp) REVERT: A 746 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: A 1043 MET cc_start: 0.8059 (pmm) cc_final: 0.6940 (tmm) REVERT: A 1180 ASP cc_start: 0.9001 (t0) cc_final: 0.8776 (t0) REVERT: A 1189 GLU cc_start: 0.9098 (tp30) cc_final: 0.8809 (tp30) REVERT: A 1312 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8782 (mt) outliers start: 19 outliers final: 12 residues processed: 97 average time/residue: 0.0767 time to fit residues: 12.1177 Evaluate side-chains 97 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.107285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074435 restraints weight = 34229.270| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.25 r_work: 0.3228 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12399 Z= 0.112 Angle : 0.558 11.180 17325 Z= 0.296 Chirality : 0.039 0.263 2009 Planarity : 0.003 0.050 1736 Dihedral : 20.621 146.759 3042 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 1.83 % Allowed : 15.46 % Favored : 82.71 % 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: 0.66 (0.25), residues: 1129 helix: 1.16 (0.22), residues: 588 sheet: -0.03 (0.52), residues: 109 loop : -0.33 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 967 TYR 0.017 0.001 TYR A1201 PHE 0.012 0.001 PHE A 966 TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (12399) covalent geometry : angle 0.55787 / 0.30 (17325) hydrogen bonds : bond 0.03795 / 4.28 ( 554) hydrogen bonds : angle 4.66873 / 4.87 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.87 seconds wall clock time: 52 minutes 53.01 seconds (3173.01 seconds total)