Starting phenix.real_space_refine on Sat Aug 23 16:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6o_41073/08_2025/8t6o_41073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6o_41073/08_2025/8t6o_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_2025/8t6o_41073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6o_41073/08_2025/8t6o_41073.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6o_41073/08_2025/8t6o_41073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6o_41073/08_2025/8t6o_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-2.0-5787/lib/python3.9/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: 2.70, per 1000 atoms: 0.23 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: 1.03 Conformation dependent library (CDL) restraints added in 493.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.40 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: 3.22 Time building geometry restraints manager: 1.32 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=" C ASN A 199 " pdb=" O ASN A 199 " ideal model delta sigma weight residual 1.235 1.252 -0.018 4.70e-03 4.53e+04 1.40e+01 bond pdb=" N PRO A 731 " pdb=" CA PRO A 731 " ideal model delta sigma weight residual 1.469 1.426 0.043 1.28e-02 6.10e+03 1.13e+01 bond pdb=" N ASN A 692 " pdb=" CA ASN A 692 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.20e+00 ... (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=" CA LYS A1325 " pdb=" CB LYS A1325 " pdb=" CG LYS A1325 " ideal model delta sigma weight residual 114.10 126.34 -12.24 2.00e+00 2.50e-01 3.75e+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: 1616 0.066 - 0.133: 334 0.133 - 0.199: 48 0.199 - 0.265: 8 0.265 - 0.331: 3 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' 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 chirality pdb=" CG LEU A 244 " pdb=" CB LEU A 244 " pdb=" CD1 LEU A 244 " pdb=" CD2 LEU A 244 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+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: 3.600 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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= 0.308 Angle : 1.230 71.848 17325 Z= 0.624 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 aren 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 covalent geometry : bond 0.00927 (12399) covalent geometry : angle 1.23037 (17325) hydrogen bonds : bond 0.16116 ( 554) hydrogen bonds : angle 7.06848 ( 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: 0.8439 (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: 0.1014 time to fit residues: 19.7532 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 : 0.502 ------------------------------------------------------------------------------- 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.109147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.076147 restraints weight = 33782.707| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.30 r_work: 0.3244 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 12399 Z= 0.179 Angle : 0.654 8.225 17325 Z= 0.356 Chirality : 0.040 0.205 2009 Planarity : 0.004 0.075 1736 Dihedral : 20.845 142.084 3042 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.63 % Allowed : 11.50 % Favored : 86.88 % 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 aren not related in a simple way. whole: -0.17 (0.24), residues: 1129 helix: 0.28 (0.21), residues: 579 sheet: -0.31 (0.44), residues: 119 loop : -0.40 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 494 TYR 0.017 0.002 TYR A 362 PHE 0.024 0.002 PHE A1313 TRP 0.011 0.001 TRP A1136 HIS 0.005 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00393 (12399) covalent geometry : angle 0.65350 (17325) hydrogen bonds : bond 0.04920 ( 554) hydrogen bonds : angle 5.30539 ( 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 118 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.9217 (m-40) cc_final: 0.8571 (m-40) REVERT: A 263 LYS cc_start: 0.9445 (tttp) cc_final: 0.9109 (mmtt) REVERT: A 370 GLU cc_start: 0.8196 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 670 ILE cc_start: 0.7933 (mm) cc_final: 0.7636 (mp) REVERT: A 763 MET cc_start: 0.9021 (tpp) cc_final: 0.8343 (mtp) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 0.0902 time to fit residues: 15.4303 Evaluate side-chains 103 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 113 optimal weight: 0.0010 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4005 r_free = 0.4005 target = 0.108395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075296 restraints weight = 34105.384| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.31 r_work: 0.3230 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12399 Z= 0.158 Angle : 0.593 9.835 17325 Z= 0.321 Chirality : 0.039 0.200 2009 Planarity : 0.004 0.055 1736 Dihedral : 20.806 142.990 3042 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.14 % Allowed : 11.70 % Favored : 86.16 % 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 aren not related in a simple way. whole: 0.13 (0.24), residues: 1129 helix: 0.67 (0.21), residues: 587 sheet: -0.34 (0.45), residues: 120 loop : -0.44 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.018 0.001 TYR A 362 PHE 0.010 0.001 PHE A 491 TRP 0.009 0.001 TRP A1136 HIS 0.007 0.001 HIS A 982 Details of bonding type rmsd covalent geometry : bond 0.00344 (12399) covalent geometry : angle 0.59307 (17325) hydrogen bonds : bond 0.04214 ( 554) hydrogen bonds : angle 4.89972 ( 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 125 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8688 (tp30) cc_final: 0.8474 (tp30) REVERT: A 251 ASN cc_start: 0.9220 (m-40) cc_final: 0.8327 (m-40) REVERT: A 261 ASP cc_start: 0.8571 (m-30) cc_final: 0.8252 (m-30) REVERT: A 263 LYS cc_start: 0.9464 (tttp) cc_final: 0.9104 (mmtt) REVERT: A 524 LEU cc_start: 0.8661 (pp) cc_final: 0.8366 (mm) REVERT: A 763 MET cc_start: 0.8968 (tpp) cc_final: 0.8315 (mtp) REVERT: A 930 HIS cc_start: 0.8617 (m90) cc_final: 0.8393 (m90) REVERT: A 1043 MET cc_start: 0.8004 (pmm) cc_final: 0.6823 (tmm) REVERT: A 1046 PHE cc_start: 0.8000 (m-10) cc_final: 0.7728 (m-80) REVERT: A 1180 ASP cc_start: 0.9042 (t0) cc_final: 0.8808 (t0) REVERT: A 1189 GLU cc_start: 0.9020 (tp30) cc_final: 0.8659 (tp30) outliers start: 21 outliers final: 7 residues processed: 119 average time/residue: 0.0922 time to fit residues: 16.6788 Evaluate side-chains 100 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 590 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 1092 VAL 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: 7.9990 chunk 26 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN A 990 ASN A1308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.107367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074147 restraints weight = 34171.911| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.30 r_work: 0.3214 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12399 Z= 0.146 Angle : 0.569 8.982 17325 Z= 0.305 Chirality : 0.038 0.201 2009 Planarity : 0.003 0.049 1736 Dihedral : 20.738 145.377 3042 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.44 % Allowed : 12.11 % Favored : 85.45 % 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 aren not related in a simple way. whole: 0.41 (0.25), residues: 1129 helix: 0.95 (0.22), residues: 591 sheet: -0.26 (0.47), residues: 119 loop : -0.41 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 400 TYR 0.019 0.001 TYR A 362 PHE 0.012 0.001 PHE A1258 TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A1264 Details of bonding type rmsd covalent geometry : bond 0.00315 (12399) covalent geometry : angle 0.56854 (17325) hydrogen bonds : bond 0.03863 ( 554) hydrogen bonds : angle 4.76781 ( 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 127 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8591 (tp30) cc_final: 0.8261 (tp30) REVERT: A 251 ASN cc_start: 0.9169 (m-40) cc_final: 0.8949 (m-40) REVERT: A 524 LEU cc_start: 0.8704 (pp) cc_final: 0.8366 (mm) REVERT: A 746 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: A 762 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 930 HIS cc_start: 0.8606 (m90) cc_final: 0.8326 (m90) REVERT: A 1043 MET cc_start: 0.8071 (pmm) cc_final: 0.6918 (tmm) REVERT: A 1180 ASP cc_start: 0.9031 (t0) cc_final: 0.8806 (t0) REVERT: A 1189 GLU cc_start: 0.9047 (tp30) cc_final: 0.8700 (tp30) outliers start: 24 outliers final: 12 residues processed: 119 average time/residue: 0.1114 time to fit residues: 19.3382 Evaluate side-chains 95 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 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 1266 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3989 r_free = 0.3989 target = 0.107070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074110 restraints weight = 34097.713| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.27 r_work: 0.3216 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12399 Z= 0.137 Angle : 0.560 9.104 17325 Z= 0.295 Chirality : 0.037 0.189 2009 Planarity : 0.003 0.053 1736 Dihedral : 20.674 146.578 3042 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.63 % Allowed : 13.12 % 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 aren not related in a simple way. whole: 0.60 (0.25), residues: 1129 helix: 1.12 (0.22), residues: 591 sheet: -0.12 (0.48), residues: 117 loop : -0.36 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.015 0.001 TYR A 362 PHE 0.011 0.001 PHE A 966 TRP 0.007 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00297 (12399) covalent geometry : angle 0.56034 (17325) hydrogen bonds : bond 0.03615 ( 554) hydrogen bonds : angle 4.64078 ( 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 109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8626 (tp30) cc_final: 0.8295 (tp30) REVERT: A 524 LEU cc_start: 0.8685 (pp) cc_final: 0.8367 (mm) REVERT: A 627 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 746 GLU cc_start: 0.8402 (tp30) cc_final: 0.8177 (tp30) REVERT: A 762 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7080 (tm-30) REVERT: A 763 MET cc_start: 0.8905 (tpp) cc_final: 0.8692 (tpp) REVERT: A 930 HIS cc_start: 0.8644 (m90) cc_final: 0.8345 (m90) REVERT: A 1043 MET cc_start: 0.8048 (pmm) cc_final: 0.6914 (tmm) REVERT: A 1180 ASP cc_start: 0.9032 (t0) cc_final: 0.8806 (t0) REVERT: A 1189 GLU cc_start: 0.9077 (tp30) cc_final: 0.8750 (tp30) REVERT: A 1241 HIS cc_start: 0.8448 (m90) cc_final: 0.8165 (m-70) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.0952 time to fit residues: 15.0636 Evaluate side-chains 96 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 213 SER 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 726 ASN Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4002 r_free = 0.4002 target = 0.107543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.075036 restraints weight = 34090.350| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.27 r_work: 0.3209 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12399 Z= 0.125 Angle : 0.546 8.904 17325 Z= 0.287 Chirality : 0.037 0.186 2009 Planarity : 0.003 0.052 1736 Dihedral : 20.616 147.724 3042 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 aren not related in a simple way. whole: 0.73 (0.25), residues: 1129 helix: 1.24 (0.22), residues: 591 sheet: 0.14 (0.49), residues: 110 loop : -0.39 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.015 0.001 TYR A 362 PHE 0.012 0.001 PHE A 966 TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00266 (12399) covalent geometry : angle 0.54601 (17325) hydrogen bonds : bond 0.03495 ( 554) hydrogen bonds : angle 4.61485 ( 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 107 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 60 GLU cc_start: 0.8636 (tp30) cc_final: 0.8282 (tp30) REVERT: A 524 LEU cc_start: 0.8705 (pp) cc_final: 0.8356 (mm) REVERT: A 627 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 746 GLU cc_start: 0.8419 (tp30) cc_final: 0.8211 (tp30) REVERT: A 762 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 930 HIS cc_start: 0.8630 (m90) cc_final: 0.8182 (m90) REVERT: A 1043 MET cc_start: 0.8075 (pmm) cc_final: 0.6790 (tmm) REVERT: A 1180 ASP cc_start: 0.9041 (t0) cc_final: 0.8819 (t0) REVERT: A 1189 GLU cc_start: 0.9094 (tp30) cc_final: 0.8776 (tp30) outliers start: 19 outliers final: 13 residues processed: 102 average time/residue: 0.0904 time to fit residues: 14.6439 Evaluate side-chains 100 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 255 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A 726 ASN A1241 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.106393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.073855 restraints weight = 33808.198| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.20 r_work: 0.3187 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3809 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= 0.149 Angle : 0.548 8.117 17325 Z= 0.290 Chirality : 0.037 0.187 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.586 148.904 3042 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 2.95 % Allowed : 13.43 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1129 helix: 1.35 (0.22), residues: 585 sheet: -0.02 (0.48), residues: 115 loop : -0.40 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.017 0.001 TYR A1201 PHE 0.012 0.001 PHE A 966 TRP 0.006 0.001 TRP A 464 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00322 (12399) covalent geometry : angle 0.54763 (17325) hydrogen bonds : bond 0.03646 ( 554) hydrogen bonds : angle 4.61441 ( 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 119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8662 (tp30) cc_final: 0.8304 (tp30) REVERT: A 110 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7629 (p0) REVERT: A 304 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: A 524 LEU cc_start: 0.8765 (pp) cc_final: 0.8386 (mm) REVERT: A 627 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 634 GLU cc_start: 0.9266 (tp30) cc_final: 0.8960 (tm-30) REVERT: A 1043 MET cc_start: 0.8133 (pmm) cc_final: 0.7042 (tmm) REVERT: A 1046 PHE cc_start: 0.7781 (m-10) cc_final: 0.7425 (m-80) REVERT: A 1180 ASP cc_start: 0.9069 (t0) cc_final: 0.8857 (t0) REVERT: A 1189 GLU cc_start: 0.9129 (tp30) cc_final: 0.8826 (tp30) REVERT: A 1241 HIS cc_start: 0.8393 (m170) cc_final: 0.8166 (m-70) outliers start: 29 outliers final: 14 residues processed: 111 average time/residue: 0.0965 time to fit residues: 16.6132 Evaluate side-chains 99 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 494 ARG 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 997 LEU 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: 1.9990 chunk 101 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 712 GLN 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 = 0.106856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.074362 restraints weight = 33835.954| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.23 r_work: 0.3194 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4064 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= 0.133 Angle : 0.541 10.143 17325 Z= 0.283 Chirality : 0.037 0.174 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.564 150.548 3042 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.24 % Allowed : 14.34 % Favored : 83.42 % 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 aren not related in a simple way. whole: 0.82 (0.25), residues: 1129 helix: 1.40 (0.22), residues: 585 sheet: 0.05 (0.59), residues: 85 loop : -0.41 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.014 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 covalent geometry : bond 0.00287 (12399) covalent geometry : angle 0.54072 (17325) hydrogen bonds : bond 0.03525 ( 554) hydrogen bonds : angle 4.55947 ( 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 119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7280 (p90) cc_final: 0.6934 (p90) REVERT: A 51 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8271 (tt) REVERT: A 60 GLU cc_start: 0.8649 (tp30) cc_final: 0.8303 (tp30) REVERT: A 110 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 304 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: A 524 LEU cc_start: 0.8800 (pp) cc_final: 0.8382 (mm) REVERT: A 627 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7401 (mm-30) REVERT: A 959 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7660 (pttt) REVERT: A 1043 MET cc_start: 0.8121 (pmm) cc_final: 0.6849 (tmm) REVERT: A 1046 PHE cc_start: 0.7756 (m-10) cc_final: 0.7219 (m-80) REVERT: A 1180 ASP cc_start: 0.9032 (t0) cc_final: 0.8805 (t0) REVERT: A 1189 GLU cc_start: 0.9102 (tp30) cc_final: 0.8838 (tp30) REVERT: A 1241 HIS cc_start: 0.8424 (m170) cc_final: 0.8153 (m-70) outliers start: 22 outliers final: 15 residues processed: 113 average time/residue: 0.0978 time to fit residues: 16.9042 Evaluate side-chains 108 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1305 GLN 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: 3.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 GLN A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.106416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073573 restraints weight = 33570.022| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.23 r_work: 0.3188 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4215 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= 0.132 Angle : 0.548 10.267 17325 Z= 0.287 Chirality : 0.037 0.192 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.523 153.193 3042 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 2.03 % Allowed : 15.16 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1129 helix: 1.36 (0.22), residues: 591 sheet: 0.31 (0.63), residues: 79 loop : -0.42 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.018 0.001 TYR A1201 PHE 0.012 0.001 PHE A 966 TRP 0.005 0.001 TRP A1074 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00285 (12399) covalent geometry : angle 0.54826 (17325) hydrogen bonds : bond 0.03574 ( 554) hydrogen bonds : angle 4.60102 ( 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 111 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7238 (p90) cc_final: 0.7033 (p90) REVERT: A 51 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 60 GLU cc_start: 0.8631 (tp30) cc_final: 0.8285 (tp30) REVERT: A 110 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7639 (p0) REVERT: A 304 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: A 524 LEU cc_start: 0.8803 (pp) cc_final: 0.8365 (mm) REVERT: A 627 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 634 GLU cc_start: 0.9271 (tp30) cc_final: 0.8956 (tm-30) REVERT: A 959 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7706 (pttt) REVERT: A 1043 MET cc_start: 0.8116 (pmm) cc_final: 0.6850 (tmm) REVERT: A 1046 PHE cc_start: 0.7728 (m-10) cc_final: 0.7202 (m-80) REVERT: A 1180 ASP cc_start: 0.9027 (t0) cc_final: 0.8808 (t0) REVERT: A 1189 GLU cc_start: 0.9130 (tp30) cc_final: 0.8881 (tp30) REVERT: A 1241 HIS cc_start: 0.8457 (m170) cc_final: 0.8170 (m-70) outliers start: 20 outliers final: 16 residues processed: 106 average time/residue: 0.1078 time to fit residues: 17.1370 Evaluate side-chains 107 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 726 ASN Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1305 GLN 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: 0.6980 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 0.0060 chunk 21 optimal weight: 0.2980 chunk 80 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 98 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 GLN A 726 ASN A 940 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.108120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075775 restraints weight = 34029.138| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.28 r_work: 0.3234 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12399 Z= 0.108 Angle : 0.547 10.938 17325 Z= 0.284 Chirality : 0.036 0.158 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.498 154.834 3042 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 1.63 % Allowed : 16.07 % Favored : 82.30 % 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 aren not related in a simple way. whole: 0.84 (0.25), residues: 1129 helix: 1.36 (0.22), residues: 591 sheet: 0.28 (0.62), residues: 79 loop : -0.36 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.013 0.001 TYR A 362 PHE 0.011 0.001 PHE A 966 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00228 (12399) covalent geometry : angle 0.54740 (17325) hydrogen bonds : bond 0.03449 ( 554) hydrogen bonds : angle 4.53362 ( 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 109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 60 GLU cc_start: 0.8604 (tp30) cc_final: 0.8277 (tp30) REVERT: A 304 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: A 627 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 634 GLU cc_start: 0.9274 (tp30) cc_final: 0.8963 (tm-30) REVERT: A 959 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7601 (ptpt) REVERT: A 1043 MET cc_start: 0.8160 (pmm) cc_final: 0.6924 (tmm) REVERT: A 1046 PHE cc_start: 0.7707 (m-10) cc_final: 0.7184 (m-80) REVERT: A 1180 ASP cc_start: 0.9009 (t0) cc_final: 0.8791 (t0) REVERT: A 1189 GLU cc_start: 0.9155 (tp30) cc_final: 0.8887 (tp30) REVERT: A 1241 HIS cc_start: 0.8428 (m170) cc_final: 0.8140 (m-70) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.0944 time to fit residues: 15.5241 Evaluate side-chains 101 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 213 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 GLN A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.107272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075129 restraints weight = 33740.717| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.39 r_work: 0.3172 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12399 Z= 0.176 Angle : 0.583 10.508 17325 Z= 0.303 Chirality : 0.038 0.265 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.532 156.106 3042 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 1.83 % Allowed : 16.68 % Favored : 81.49 % 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 aren not related in a simple way. whole: 0.78 (0.25), residues: 1129 helix: 1.36 (0.22), residues: 583 sheet: 0.20 (0.59), residues: 85 loop : -0.43 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.018 0.001 TYR A1201 PHE 0.014 0.001 PHE A 966 TRP 0.009 0.001 TRP A1074 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00382 (12399) covalent geometry : angle 0.58277 (17325) hydrogen bonds : bond 0.03828 ( 554) hydrogen bonds : angle 4.65599 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3273.60 seconds wall clock time: 56 minutes 48.95 seconds (3408.95 seconds total)