Starting phenix.real_space_refine on Fri Jul 3 09:08:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6o_41073/07_2026/8t6o_41073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6o_41073/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t6o_41073/07_2026/8t6o_41073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6o_41073/07_2026/8t6o_41073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6o_41073/07_2026/8t6o_41073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6o_41073/07_2026/8t6o_41073.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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-dev-6108/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: 2.82, per 1000 atoms: 0.24 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 559.3 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: 1.29 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: 3.16 Time building geometry restraints manager: 1.35 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: 1607 0.066 - 0.133: 344 0.133 - 0.199: 48 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.150 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- 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= 0.412 Angle : 1.244 71.848 17325 Z= 0.747 Chirality : 0.055 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 0.00943 / 0.41 (12399) covalent geometry : angle 1.24434 / 0.75 (17325) hydrogen bonds : bond 0.16116 / 17.73 ( 554) hydrogen bonds : angle 7.06848 / 7.24 ( 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 : 0.316 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: 0.1066 time to fit residues: 21.0816 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 : 0.427 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.4027 r_free = 0.4027 target = 0.109888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.076989 restraints weight = 33695.355| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.30 r_work: 0.3259 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 12399 Z= 0.178 Angle : 0.676 8.293 17325 Z= 0.383 Chirality : 0.045 0.311 2009 Planarity : 0.004 0.067 1736 Dihedral : 20.924 140.732 3042 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.73 % Allowed : 10.68 % Favored : 87.59 % 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: -0.38 (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 0.021 0.002 TYR A1294 PHE 0.032 0.002 PHE A1313 TRP 0.012 0.001 TRP A1136 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (12399) covalent geometry : angle 0.67640 / 0.38 (17325) hydrogen bonds : bond 0.05725 / 6.24 ( 554) hydrogen bonds : angle 5.44124 / 5.74 ( 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 : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8742 (tp30) cc_final: 0.8413 (tp30) REVERT: A 251 ASN cc_start: 0.9167 (m-40) cc_final: 0.8546 (m-40) REVERT: A 263 LYS cc_start: 0.9427 (tttp) cc_final: 0.9103 (mmtt) REVERT: A 370 GLU cc_start: 0.8225 (tt0) cc_final: 0.7596 (tm-30) REVERT: A 502 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 696 LEU cc_start: 0.8181 (mt) cc_final: 0.7937 (mt) REVERT: A 763 MET cc_start: 0.9043 (tpp) cc_final: 0.8334 (mtp) REVERT: A 1312 LEU cc_start: 0.9057 (tp) cc_final: 0.8849 (mt) REVERT: A 1356 TYR cc_start: 0.8692 (m-10) cc_final: 0.8431 (m-80) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 0.0792 time to fit residues: 14.2315 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 : 0.358 ------------------------------------------------------------------------------- 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: 0.9990 chunk 113 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.110464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.078326 restraints weight = 33875.550| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.34 r_work: 0.3255 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12399 Z= 0.137 Angle : 0.594 8.404 17325 Z= 0.335 Chirality : 0.042 0.303 2009 Planarity : 0.004 0.052 1736 Dihedral : 20.886 141.674 3042 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.53 % Allowed : 11.80 % Favored : 86.67 % 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: 0.06 (0.24), residues: 1129 helix: 0.58 (0.21), residues: 584 sheet: -0.40 (0.44), residues: 120 loop : -0.42 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1114 TYR 0.018 0.001 TYR A 988 PHE 0.019 0.001 PHE A 290 TRP 0.010 0.001 TRP A1136 HIS 0.007 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (12399) covalent geometry : angle 0.59368 / 0.34 (17325) hydrogen bonds : bond 0.04870 / 5.50 ( 554) hydrogen bonds : angle 5.01812 / 5.24 ( 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 110 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8722 (tp30) cc_final: 0.8431 (tp30) REVERT: A 251 ASN cc_start: 0.9196 (m-40) cc_final: 0.8322 (m-40) REVERT: A 263 LYS cc_start: 0.9430 (tttp) cc_final: 0.9060 (mmtt) REVERT: A 370 GLU cc_start: 0.8173 (tt0) cc_final: 0.7501 (tm-30) REVERT: A 524 LEU cc_start: 0.8582 (pp) cc_final: 0.8191 (mt) REVERT: A 1043 MET cc_start: 0.7959 (pmm) cc_final: 0.6758 (tmm) REVERT: A 1046 PHE cc_start: 0.7988 (m-10) cc_final: 0.7748 (m-80) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.0900 time to fit residues: 14.7047 Evaluate side-chains 95 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1305 GLN 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: 0.8980 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 0.0030 chunk 124 optimal weight: 20.0000 chunk 94 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.9510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4031 r_free = 0.4031 target = 0.109562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.077070 restraints weight = 34101.734| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.34 r_work: 0.3234 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12399 Z= 0.141 Angle : 0.577 11.184 17325 Z= 0.324 Chirality : 0.041 0.262 2009 Planarity : 0.003 0.050 1736 Dihedral : 20.798 142.999 3042 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.03 % Allowed : 12.00 % Favored : 85.96 % 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: 0.24 (0.25), residues: 1129 helix: 0.82 (0.22), residues: 588 sheet: -0.34 (0.45), residues: 120 loop : -0.48 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.021 0.001 TYR A 362 PHE 0.009 0.001 PHE A1258 TRP 0.006 0.001 TRP A1136 HIS 0.007 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (12399) covalent geometry : angle 0.57741 / 0.32 (17325) hydrogen bonds : bond 0.04515 / 5.04 ( 554) hydrogen bonds : angle 4.89542 / 5.14 ( 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 122 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7772 (tt) REVERT: A 60 GLU cc_start: 0.8681 (tp30) cc_final: 0.8365 (tp30) REVERT: A 251 ASN cc_start: 0.9211 (m-40) cc_final: 0.8333 (m-40) REVERT: A 263 LYS cc_start: 0.9448 (tttp) cc_final: 0.9076 (mmtt) REVERT: A 627 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 1043 MET cc_start: 0.8010 (pmm) cc_final: 0.6811 (tmm) REVERT: A 1046 PHE cc_start: 0.8006 (m-10) cc_final: 0.7792 (m-10) REVERT: A 1089 MET cc_start: 0.8986 (ttm) cc_final: 0.8764 (ttp) REVERT: A 1189 GLU cc_start: 0.9011 (tp30) cc_final: 0.8648 (tp30) REVERT: A 1241 HIS cc_start: 0.8520 (m90) cc_final: 0.8164 (m-70) outliers start: 20 outliers final: 9 residues processed: 114 average time/residue: 0.0882 time to fit residues: 15.7218 Evaluate side-chains 99 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 50.0000 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 726 ASN ** A 990 ASN ** 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 = 0.4034 r_free = 0.4034 target = 0.109575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.077060 restraints weight = 34098.816| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.34 r_work: 0.3238 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2412 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= 0.128 Angle : 0.564 8.064 17325 Z= 0.314 Chirality : 0.041 0.275 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.785 144.253 3042 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 13.02 % Favored : 85.05 % 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: 0.48 (0.25), residues: 1129 helix: 0.98 (0.22), residues: 586 sheet: -0.29 (0.46), residues: 120 loop : -0.30 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.019 0.001 TYR A1201 PHE 0.014 0.001 PHE A 966 TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (12399) covalent geometry : angle 0.56358 / 0.31 (17325) hydrogen bonds : bond 0.04213 / 4.85 ( 554) hydrogen bonds : angle 4.87354 / 5.14 ( 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 110 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7946 (tt) REVERT: A 60 GLU cc_start: 0.8655 (tp30) cc_final: 0.8302 (tp30) REVERT: A 251 ASN cc_start: 0.9193 (m-40) cc_final: 0.8290 (m-40) REVERT: A 261 ASP cc_start: 0.8538 (m-30) cc_final: 0.8254 (m-30) REVERT: A 263 LYS cc_start: 0.9456 (tttp) cc_final: 0.9075 (mmtt) REVERT: A 304 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8682 (m-30) REVERT: A 524 LEU cc_start: 0.8499 (pp) cc_final: 0.8210 (mm) REVERT: A 627 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 746 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: A 763 MET cc_start: 0.9086 (tpp) cc_final: 0.8421 (mtp) REVERT: A 1043 MET cc_start: 0.8012 (pmm) cc_final: 0.6817 (tmm) REVERT: A 1089 MET cc_start: 0.9008 (ttm) cc_final: 0.8789 (ttp) REVERT: A 1180 ASP cc_start: 0.9021 (t0) cc_final: 0.8786 (t0) REVERT: A 1189 GLU cc_start: 0.9023 (tp30) cc_final: 0.8645 (tp30) outliers start: 19 outliers final: 7 residues processed: 105 average time/residue: 0.0925 time to fit residues: 14.9603 Evaluate side-chains 95 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 301 LEU 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 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 1092 VAL 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: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.107051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.074392 restraints weight = 34250.802| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.31 r_work: 0.3179 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12399 Z= 0.183 Angle : 0.580 7.708 17325 Z= 0.323 Chirality : 0.040 0.257 2009 Planarity : 0.004 0.050 1736 Dihedral : 20.788 144.765 3042 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.44 (0.25), residues: 1129 helix: 1.01 (0.22), residues: 587 sheet: -0.38 (0.47), residues: 119 loop : -0.39 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 494 TYR 0.025 0.001 TYR A 362 PHE 0.012 0.002 PHE A 966 TRP 0.006 0.001 TRP A1074 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (12399) covalent geometry : angle 0.57991 / 0.32 (17325) hydrogen bonds : bond 0.04463 / 4.95 ( 554) hydrogen bonds : angle 4.90244 / 5.21 ( 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 119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 60 GLU cc_start: 0.8710 (tp30) cc_final: 0.8343 (tp30) REVERT: A 110 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7670 (p0) REVERT: A 251 ASN cc_start: 0.9171 (m-40) cc_final: 0.8168 (m-40) REVERT: A 263 LYS cc_start: 0.9497 (tttp) cc_final: 0.9073 (mmtt) REVERT: A 304 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8769 (m-30) REVERT: A 524 LEU cc_start: 0.8768 (pp) cc_final: 0.8355 (mm) REVERT: A 627 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 746 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: A 763 MET cc_start: 0.9085 (tpp) cc_final: 0.8450 (mtp) REVERT: A 1043 MET cc_start: 0.7977 (pmm) cc_final: 0.6794 (tmm) REVERT: A 1089 MET cc_start: 0.9074 (ttm) cc_final: 0.8852 (ttp) REVERT: A 1180 ASP cc_start: 0.9086 (t0) cc_final: 0.8871 (t0) REVERT: A 1189 GLU cc_start: 0.9094 (tp30) cc_final: 0.8744 (tp30) REVERT: A 1312 LEU cc_start: 0.9083 (mt) cc_final: 0.8680 (mt) outliers start: 28 outliers final: 13 residues processed: 113 average time/residue: 0.1013 time to fit residues: 17.2475 Evaluate side-chains 101 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 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 1092 VAL Chi-restraints excluded: chain A residue 1125 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.106440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073283 restraints weight = 34183.815| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.25 r_work: 0.3190 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12399 Z= 0.170 Angle : 0.587 10.443 17325 Z= 0.321 Chirality : 0.040 0.270 2009 Planarity : 0.004 0.048 1736 Dihedral : 20.816 144.275 3042 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.14 % Allowed : 13.12 % 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: 0.48 (0.25), residues: 1129 helix: 1.09 (0.22), residues: 582 sheet: -0.33 (0.50), residues: 109 loop : -0.46 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 400 TYR 0.021 0.001 TYR A 362 PHE 0.012 0.001 PHE A 966 TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (12399) covalent geometry : angle 0.58705 / 0.32 (17325) hydrogen bonds : bond 0.04177 / 4.72 ( 554) hydrogen bonds : angle 4.87192 / 5.19 ( 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 112 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 60 GLU cc_start: 0.8718 (tp30) cc_final: 0.8356 (tp30) REVERT: A 110 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7671 (p0) REVERT: A 251 ASN cc_start: 0.9148 (m-40) cc_final: 0.8852 (m-40) REVERT: A 263 LYS cc_start: 0.9502 (tttp) cc_final: 0.9301 (mtpp) REVERT: A 304 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8721 (m-30) REVERT: A 524 LEU cc_start: 0.8646 (pp) cc_final: 0.8289 (mm) REVERT: A 627 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 746 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: A 763 MET cc_start: 0.9038 (tpp) cc_final: 0.8470 (mtp) REVERT: A 1043 MET cc_start: 0.8028 (pmm) cc_final: 0.6870 (tmm) REVERT: A 1089 MET cc_start: 0.9040 (ttm) cc_final: 0.8821 (ttp) REVERT: A 1180 ASP cc_start: 0.9038 (t0) cc_final: 0.8825 (t0) REVERT: A 1189 GLU cc_start: 0.9072 (tp30) cc_final: 0.8759 (tp30) REVERT: A 1312 LEU cc_start: 0.9194 (mt) cc_final: 0.8759 (mt) outliers start: 21 outliers final: 11 residues processed: 106 average time/residue: 0.0892 time to fit residues: 14.6364 Evaluate side-chains 99 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 362 TYR 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 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 1092 VAL 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: 0.8980 chunk 101 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 118 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.107394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074406 restraints weight = 34194.012| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.25 r_work: 0.3219 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12399 Z= 0.122 Angle : 0.565 10.836 17325 Z= 0.306 Chirality : 0.039 0.268 2009 Planarity : 0.003 0.047 1736 Dihedral : 20.800 144.632 3042 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 1.93 % Allowed : 13.84 % 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: 0.63 (0.25), residues: 1129 helix: 1.18 (0.22), residues: 586 sheet: -0.20 (0.50), residues: 109 loop : -0.36 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 400 TYR 0.020 0.001 TYR A 362 PHE 0.012 0.001 PHE A 491 TRP 0.006 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (12399) covalent geometry : angle 0.56487 / 0.31 (17325) hydrogen bonds : bond 0.03917 / 4.45 ( 554) hydrogen bonds : angle 4.78146 / 5.05 ( 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 112 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 60 GLU cc_start: 0.8666 (tp30) cc_final: 0.8284 (tp30) REVERT: A 251 ASN cc_start: 0.9180 (m-40) cc_final: 0.7005 (m-40) REVERT: A 261 ASP cc_start: 0.8850 (p0) cc_final: 0.7875 (t0) REVERT: A 263 LYS cc_start: 0.9488 (tttp) cc_final: 0.8757 (mmtm) REVERT: A 276 ASP cc_start: 0.9344 (m-30) cc_final: 0.9137 (m-30) REVERT: A 304 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8648 (m-30) REVERT: A 524 LEU cc_start: 0.8633 (pp) cc_final: 0.8262 (mm) REVERT: A 627 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 746 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: A 763 MET cc_start: 0.9014 (tpp) cc_final: 0.8426 (mtp) REVERT: A 1043 MET cc_start: 0.8023 (pmm) cc_final: 0.6872 (tmm) REVERT: A 1180 ASP cc_start: 0.9004 (t0) cc_final: 0.8785 (t0) REVERT: A 1189 GLU cc_start: 0.9055 (tp30) cc_final: 0.8753 (tp30) REVERT: A 1312 LEU cc_start: 0.9188 (mt) cc_final: 0.8755 (mt) outliers start: 19 outliers final: 9 residues processed: 106 average time/residue: 0.0873 time to fit residues: 14.1473 Evaluate side-chains 97 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain A residue 304 ASP 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 616 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 106 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 123 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 116 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN A1241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.107484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074474 restraints weight = 33786.985| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.26 r_work: 0.3210 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12399 Z= 0.122 Angle : 0.555 11.120 17325 Z= 0.301 Chirality : 0.039 0.264 2009 Planarity : 0.003 0.047 1736 Dihedral : 20.759 145.885 3042 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.14 % Allowed : 13.53 % Favored : 84.33 % 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: 1.19 (0.22), residues: 587 sheet: -0.14 (0.50), residues: 109 loop : -0.34 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.019 0.001 TYR A 362 PHE 0.013 0.001 PHE A1258 TRP 0.006 0.001 TRP A 464 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (12399) covalent geometry : angle 0.55510 / 0.30 (17325) hydrogen bonds : bond 0.03859 / 4.36 ( 554) hydrogen bonds : angle 4.76404 / 5.02 ( 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 110 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 60 GLU cc_start: 0.8675 (tp30) cc_final: 0.8271 (tp30) REVERT: A 110 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7615 (p0) REVERT: A 251 ASN cc_start: 0.9168 (m-40) cc_final: 0.6780 (m-40) REVERT: A 261 ASP cc_start: 0.8858 (p0) cc_final: 0.7933 (t0) REVERT: A 263 LYS cc_start: 0.9480 (tttp) cc_final: 0.8759 (mmtm) REVERT: A 304 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8699 (m-30) REVERT: A 524 LEU cc_start: 0.8647 (pp) cc_final: 0.8261 (mm) REVERT: A 627 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 746 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: A 763 MET cc_start: 0.9011 (tpp) cc_final: 0.8425 (mtp) REVERT: A 1043 MET cc_start: 0.8021 (pmm) cc_final: 0.6871 (tmm) REVERT: A 1180 ASP cc_start: 0.9012 (t0) cc_final: 0.8797 (t0) REVERT: A 1189 GLU cc_start: 0.9090 (tp30) cc_final: 0.8782 (tp30) REVERT: A 1312 LEU cc_start: 0.9182 (mt) cc_final: 0.8737 (mt) outliers start: 21 outliers final: 11 residues processed: 105 average time/residue: 0.0893 time to fit residues: 14.7815 Evaluate side-chains 98 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 1125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 77 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.107871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075280 restraints weight = 33949.612| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.26 r_work: 0.3226 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12399 Z= 0.113 Angle : 0.568 12.095 17325 Z= 0.302 Chirality : 0.039 0.258 2009 Planarity : 0.003 0.048 1736 Dihedral : 20.711 147.021 3042 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 1.73 % Allowed : 14.04 % 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: 0.68 (0.25), residues: 1129 helix: 1.22 (0.22), residues: 587 sheet: -0.24 (0.50), residues: 109 loop : -0.32 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.018 0.001 TYR A 362 PHE 0.013 0.001 PHE A 966 TRP 0.006 0.001 TRP A 464 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (12399) covalent geometry : angle 0.56828 / 0.30 (17325) hydrogen bonds : bond 0.03804 / 4.33 ( 554) hydrogen bonds : angle 4.68968 / 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 104 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8069 (tt) REVERT: A 110 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7564 (p0) REVERT: A 251 ASN cc_start: 0.9179 (m-40) cc_final: 0.8905 (m-40) REVERT: A 261 ASP cc_start: 0.8869 (p0) cc_final: 0.8507 (p0) REVERT: A 263 LYS cc_start: 0.9471 (tttp) cc_final: 0.9248 (mtpp) REVERT: A 524 LEU cc_start: 0.8640 (pp) cc_final: 0.8271 (mm) REVERT: A 627 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 746 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: A 763 MET cc_start: 0.8977 (tpp) cc_final: 0.8385 (mtp) REVERT: A 1043 MET cc_start: 0.8040 (pmm) cc_final: 0.6930 (tmm) REVERT: A 1180 ASP cc_start: 0.9033 (t0) cc_final: 0.8821 (t0) REVERT: A 1189 GLU cc_start: 0.9102 (tp30) cc_final: 0.8806 (tp30) REVERT: A 1312 LEU cc_start: 0.9174 (mt) cc_final: 0.8744 (mt) outliers start: 17 outliers final: 7 residues processed: 100 average time/residue: 0.0885 time to fit residues: 14.1272 Evaluate side-chains 92 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 746 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN A 255 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.107624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.075033 restraints weight = 33811.529| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.25 r_work: 0.3221 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12399 Z= 0.118 Angle : 0.555 11.382 17325 Z= 0.297 Chirality : 0.039 0.249 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.667 147.855 3042 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 1.63 % Allowed : 15.06 % 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: 0.69 (0.25), residues: 1129 helix: 1.21 (0.22), residues: 587 sheet: -0.21 (0.50), residues: 109 loop : -0.29 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.019 0.001 TYR A 362 PHE 0.014 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 0.00244 / 0.12 (12399) covalent geometry : angle 0.55454 / 0.30 (17325) hydrogen bonds : bond 0.03770 / 4.27 ( 554) hydrogen bonds : angle 4.70198 / 4.91 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.52 seconds wall clock time: 58 minutes 18.10 seconds (3498.10 seconds total)