Starting phenix.real_space_refine on Sat Sep 12 06:00:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4i_14498/09_2026/7z4i_14498.cif" } resolution = 3.12 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 134 5.49 5 S 22 5.16 5 C 8290 2.51 5 N 2417 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13820 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2055 Classifications: {'RNAv2': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 83} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 565 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 249 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT%5*END:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 10949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10949 Classifications: {'peptide': 1338} Link IDs: {'PTRANS': 35, 'TRANS': 1302} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.07, per 1000 atoms: 0.22 Number of scatterers: 13820 At special positions: 0 Unit cell: (90.35, 123.5, 120.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 22 16.00 P 134 15.00 O 2955 8.00 N 2417 7.00 C 8290 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: 1.13 Conformation dependent library (CDL) restraints added in 531.0 milliseconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 54.5% alpha, 9.7% beta 49 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 5.222A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.621A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.738A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 282 Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.219A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 382 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.527A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.159A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 496 removed outlier: 4.109A pdb=" N MET B 495 " --> pdb=" O PHE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 526 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.554A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.631A pdb=" N LEU B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 removed outlier: 3.571A pdb=" N ILE B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.671A pdb=" N ARG B 653 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 702 through 712 removed outlier: 4.486A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 removed outlier: 3.780A pdb=" N HIS B 799 " --> pdb=" O ILE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.681A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 909 through 919 Processing helix chain 'B' and resid 925 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.970A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.238A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1032 through 1041 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.595A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1229 through 1241 removed outlier: 3.571A pdb=" N HIS B1241 " --> pdb=" O TYR B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1263 through 1280 removed outlier: 4.305A pdb=" N ASP B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 removed outlier: 3.526A pdb=" N PHE B1313 " --> pdb=" O ILE B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1316 No H-bonds generated for 'chain 'B' and resid 1314 through 1316' Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 958 removed outlier: 6.238A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 958 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 761 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.873A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.146A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 528 through 531 Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'B' and resid 943 through 944 removed outlier: 3.708A pdb=" N LYS B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AA8, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 3.911A pdb=" N TRP B1074 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AB1, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB2, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB3, first strand: chain 'B' and resid 1324 through 1326 528 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 232 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2499 1.33 - 1.45: 4103 1.45 - 1.57: 7443 1.57 - 1.69: 268 1.69 - 1.81: 42 Bond restraints: 14355 Sorted by residual: bond pdb=" N ASN B 77 " pdb=" CA ASN B 77 " ideal model delta sigma weight residual 1.458 1.407 0.052 1.26e-02 6.30e+03 1.68e+01 bond pdb=" C3' DC C -1 " pdb=" O3' DC C -1 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" CA SER B1109 " pdb=" C SER B1109 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C LYS B 76 " pdb=" N ASN B 77 " ideal model delta sigma weight residual 1.334 1.289 0.045 1.43e-02 4.89e+03 1.01e+01 bond pdb=" C3' DG C 1 " pdb=" O3' DG C 1 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.56e+00 ... (remaining 14350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 18917 1.12 - 2.25: 665 2.25 - 3.37: 301 3.37 - 4.49: 54 4.49 - 5.62: 24 Bond angle restraints: 19961 Sorted by residual: angle pdb=" O4' DC C 7 " pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.42e+01 angle pdb=" N ASN B 77 " pdb=" CA ASN B 77 " pdb=" C ASN B 77 " ideal model delta sigma weight residual 111.69 106.27 5.42 1.23e+00 6.61e-01 1.94e+01 angle pdb=" O4' DT C 4 " pdb=" C4' DT C 4 " pdb=" C3' DT C 4 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 19956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.05: 7801 27.05 - 54.10: 503 54.10 - 81.15: 128 81.15 - 108.20: 4 108.20 - 135.25: 1 Dihedral angle restraints: 8437 sinusoidal: 4500 harmonic: 3937 Sorted by residual: dihedral pdb=" C4' G A 43 " pdb=" C3' G A 43 " pdb=" C2' G A 43 " pdb=" C1' G A 43 " ideal model delta sinusoidal sigma weight residual 36.34 -37.18 73.52 1 3.10e+00 1.04e-01 7.16e+02 dihedral pdb=" C4' U A 44 " pdb=" C3' U A 44 " pdb=" C2' U A 44 " pdb=" C1' U A 44 " ideal model delta sinusoidal sigma weight residual 36.34 -37.04 73.39 1 3.10e+00 1.04e-01 7.13e+02 dihedral pdb=" C4' G A 89 " pdb=" C3' G A 89 " pdb=" C2' G A 89 " pdb=" C1' G A 89 " ideal model delta sinusoidal sigma weight residual 36.34 -36.91 73.25 1 3.10e+00 1.04e-01 7.11e+02 ... (remaining 8434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1902 0.058 - 0.115: 240 0.115 - 0.173: 24 0.173 - 0.231: 83 0.231 - 0.288: 36 Chirality restraints: 2285 Sorted by residual: chirality pdb=" C2' U A 44 " pdb=" C3' U A 44 " pdb=" O2' U A 44 " pdb=" C1' U A 44 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' G A 81 " pdb=" C3' G A 81 " pdb=" O2' G A 81 " pdb=" C1' G A 81 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' C A 55 " pdb=" C3' C A 55 " pdb=" O2' C A 55 " pdb=" C1' C A 55 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2282 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 980 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C ASN B 980 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN B 980 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR B 981 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1273 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ILE B1273 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE B1273 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B1274 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 76 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C LYS B 76 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS B 76 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 77 " -0.011 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 3794 2.82 - 3.40: 14916 3.40 - 3.98: 29195 3.98 - 4.56: 39302 4.56 - 5.14: 53744 Nonbonded interactions: 140951 Sorted by model distance: nonbonded pdb=" O2' A A 47 " pdb=" O LEU B 101 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR B1232 " pdb=" OE1 GLU B1268 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP B1361 " pdb=" OG SER B1363 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN B 14 " pdb=" OG SER B 55 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.263 3.040 ... (remaining 140946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.920 Find NCS groups from input model: 0.060 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.004 0.052 14355 Z= 0.273 Angle : 0.610 5.617 19961 Z= 0.361 Chirality : 0.064 0.288 2285 Planarity : 0.004 0.044 2055 Dihedral : 16.922 135.253 5889 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.58 % Allowed : 5.91 % Favored : 93.51 % 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: 0.81 (0.23), residues: 1330 helix: 1.18 (0.20), residues: 668 sheet: -0.27 (0.45), residues: 135 loop : 0.08 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 653 TYR 0.010 0.001 TYR B 155 PHE 0.010 0.001 PHE B1046 TRP 0.004 0.001 TRP B 464 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.27 (14355) covalent geometry : angle 0.61031 / 0.36 (19961) hydrogen bonds : bond 0.12956 / 6.63 ( 640) hydrogen bonds : angle 5.33417 / 2.22 ( 1756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 LEU cc_start: 0.8689 (tp) cc_final: 0.8312 (tp) REVERT: B 263 LYS cc_start: 0.9151 (mttt) cc_final: 0.8950 (mmmm) REVERT: B 470 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7443 (tp30) REVERT: B 610 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8078 (tp30) REVERT: B 795 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8105 (tt) REVERT: B 879 MET cc_start: 0.7247 (mmm) cc_final: 0.6935 (tpp) REVERT: B 911 LEU cc_start: 0.9610 (mt) cc_final: 0.9390 (tp) REVERT: B 1037 PHE cc_start: 0.8485 (p90) cc_final: 0.7947 (p90) outliers start: 7 outliers final: 2 residues processed: 135 average time/residue: 0.1514 time to fit residues: 27.7760 Evaluate side-chains 61 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1145 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 HIS B 807 GLN B 826 GLN B 854 ASN B 926 GLN B1041 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.085487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.060533 restraints weight = 48993.809| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.59 r_work: 0.3073 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14355 Z= 0.189 Angle : 0.898 21.616 19961 Z= 0.398 Chirality : 0.082 1.290 2285 Planarity : 0.004 0.063 2055 Dihedral : 16.999 134.572 3047 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.92 % Allowed : 9.57 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1330 helix: 1.46 (0.20), residues: 686 sheet: 0.01 (0.47), residues: 126 loop : 0.02 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 457 TYR 0.021 0.001 TYR B1010 PHE 0.017 0.001 PHE B 196 TRP 0.005 0.001 TRP B 883 HIS 0.010 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (14355) covalent geometry : angle 0.89815 / 0.40 (19961) hydrogen bonds : bond 0.04361 / 2.27 ( 640) hydrogen bonds : angle 4.39349 / 1.79 ( 1756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 470 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7555 (tp30) REVERT: B 495 MET cc_start: 0.8995 (mtm) cc_final: 0.8782 (mtt) REVERT: B 610 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8200 (tp30) REVERT: B 642 LEU cc_start: 0.7975 (mt) cc_final: 0.7758 (mp) REVERT: B 810 LYS cc_start: 0.7306 (mmtp) cc_final: 0.6694 (tttt) REVERT: B 882 TYR cc_start: 0.7188 (t80) cc_final: 0.6734 (t80) REVERT: B 911 LEU cc_start: 0.9608 (mt) cc_final: 0.9395 (tp) REVERT: B 933 GLN cc_start: 0.9298 (tt0) cc_final: 0.8826 (tm-30) REVERT: B 1037 PHE cc_start: 0.8582 (p90) cc_final: 0.7992 (p90) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.1555 time to fit residues: 15.2987 Evaluate side-chains 53 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 37 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 712 GLN B 826 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.082151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057438 restraints weight = 48650.430| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.45 r_work: 0.2979 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 14355 Z= 0.303 Angle : 0.796 14.348 19961 Z= 0.372 Chirality : 0.063 0.990 2285 Planarity : 0.004 0.069 2055 Dihedral : 17.398 143.118 3045 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 10.65 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1330 helix: 1.49 (0.20), residues: 678 sheet: 0.11 (0.49), residues: 126 loop : -0.09 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 919 TYR 0.041 0.002 TYR B1039 PHE 0.022 0.002 PHE B1008 TRP 0.004 0.001 TRP B 18 HIS 0.010 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.30 (14355) covalent geometry : angle 0.79636 / 0.37 (19961) hydrogen bonds : bond 0.04600 / 2.40 ( 640) hydrogen bonds : angle 4.36285 / 1.77 ( 1756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8582 (mtp) cc_final: 0.8343 (mtp) REVERT: B 610 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8411 (tp30) REVERT: B 810 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7072 (tttt) REVERT: B 882 TYR cc_start: 0.7088 (t80) cc_final: 0.6850 (t80) REVERT: B 933 GLN cc_start: 0.9345 (tt0) cc_final: 0.8859 (tm-30) REVERT: B 1037 PHE cc_start: 0.8536 (p90) cc_final: 0.7820 (p90) REVERT: B 1273 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9027 (mp) outliers start: 18 outliers final: 11 residues processed: 67 average time/residue: 0.1199 time to fit residues: 12.0816 Evaluate side-chains 55 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1273 ILE Chi-restraints excluded: chain B residue 1318 LEU Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 90 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 511 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.084061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058969 restraints weight = 48833.148| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.57 r_work: 0.3014 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14355 Z= 0.135 Angle : 0.637 10.254 19961 Z= 0.301 Chirality : 0.055 0.671 2285 Planarity : 0.003 0.043 2055 Dihedral : 17.222 138.467 3045 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.41 % Allowed : 10.82 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1330 helix: 1.72 (0.20), residues: 679 sheet: 0.14 (0.49), residues: 126 loop : -0.02 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 691 TYR 0.017 0.001 TYR B 155 PHE 0.018 0.001 PHE B 569 TRP 0.006 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14355) covalent geometry : angle 0.63686 / 0.30 (19961) hydrogen bonds : bond 0.03825 / 1.99 ( 640) hydrogen bonds : angle 4.10517 / 1.66 ( 1756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8603 (mtp) cc_final: 0.8376 (mtp) REVERT: B 610 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8337 (tp30) REVERT: B 682 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6259 (t80) REVERT: B 810 LYS cc_start: 0.7633 (mmtp) cc_final: 0.6982 (tttt) REVERT: B 1037 PHE cc_start: 0.8485 (p90) cc_final: 0.7780 (p90) outliers start: 17 outliers final: 8 residues processed: 60 average time/residue: 0.1181 time to fit residues: 10.5989 Evaluate side-chains 50 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 556 ASN B 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.080949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055468 restraints weight = 49210.292| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.48 r_work: 0.2923 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14355 Z= 0.318 Angle : 0.779 13.747 19961 Z= 0.365 Chirality : 0.058 0.754 2285 Planarity : 0.004 0.042 2055 Dihedral : 17.295 142.672 3044 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.58 % Allowed : 10.73 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1330 helix: 1.55 (0.20), residues: 681 sheet: 0.35 (0.51), residues: 124 loop : -0.13 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 586 TYR 0.019 0.002 TYR B 136 PHE 0.017 0.002 PHE B 98 TRP 0.005 0.001 TRP B 18 HIS 0.010 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.32 (14355) covalent geometry : angle 0.77950 / 0.36 (19961) hydrogen bonds : bond 0.04600 / 2.41 ( 640) hydrogen bonds : angle 4.28982 / 1.74 ( 1756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8716 (mtp) cc_final: 0.8487 (mtp) REVERT: B 682 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6482 (t80) REVERT: B 810 LYS cc_start: 0.7655 (mmtp) cc_final: 0.7009 (tttt) REVERT: B 976 ARG cc_start: 0.9023 (mtm-85) cc_final: 0.8647 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7932 (p90) outliers start: 19 outliers final: 11 residues processed: 58 average time/residue: 0.1223 time to fit residues: 10.7183 Evaluate side-chains 54 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 119 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.083048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057814 restraints weight = 48480.989| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.57 r_work: 0.2987 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14355 Z= 0.133 Angle : 0.610 10.319 19961 Z= 0.291 Chirality : 0.052 0.628 2285 Planarity : 0.003 0.037 2055 Dihedral : 17.120 140.952 3044 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.08 % Allowed : 11.98 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1330 helix: 1.85 (0.20), residues: 676 sheet: 0.33 (0.50), residues: 126 loop : -0.09 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1298 TYR 0.024 0.001 TYR B 823 PHE 0.008 0.001 PHE B 518 TRP 0.006 0.001 TRP B 476 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14355) covalent geometry : angle 0.60978 / 0.29 (19961) hydrogen bonds : bond 0.03716 / 1.93 ( 640) hydrogen bonds : angle 4.03420 / 1.64 ( 1756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8177 (mm) REVERT: B 383 MET cc_start: 0.8676 (mtp) cc_final: 0.8449 (mtp) REVERT: B 682 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6348 (t80) REVERT: B 762 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 810 LYS cc_start: 0.7671 (mmtp) cc_final: 0.7027 (tttt) REVERT: B 976 ARG cc_start: 0.9001 (mtm-85) cc_final: 0.8599 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7992 (p90) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 0.1248 time to fit residues: 10.4938 Evaluate side-chains 50 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.082036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056836 restraints weight = 48790.971| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.56 r_work: 0.2958 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14355 Z= 0.189 Angle : 0.628 10.323 19961 Z= 0.299 Chirality : 0.051 0.593 2285 Planarity : 0.003 0.038 2055 Dihedral : 17.121 142.236 3044 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.50 % Allowed : 12.06 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1330 helix: 1.82 (0.20), residues: 680 sheet: 0.49 (0.51), residues: 123 loop : -0.10 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1298 TYR 0.022 0.001 TYR B 882 PHE 0.020 0.001 PHE B 518 TRP 0.005 0.001 TRP B 883 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (14355) covalent geometry : angle 0.62763 / 0.30 (19961) hydrogen bonds : bond 0.03857 / 2.01 ( 640) hydrogen bonds : angle 4.03395 / 1.65 ( 1756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 383 MET cc_start: 0.8735 (mtp) cc_final: 0.8506 (mtp) REVERT: B 682 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6457 (t80) REVERT: B 762 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 810 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7075 (tttt) REVERT: B 823 TYR cc_start: 0.7217 (m-80) cc_final: 0.6988 (m-80) REVERT: B 976 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8620 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7946 (p90) outliers start: 18 outliers final: 10 residues processed: 59 average time/residue: 0.1145 time to fit residues: 10.1569 Evaluate side-chains 56 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 2 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.078942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053729 restraints weight = 49069.830| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.48 r_work: 0.2873 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 14355 Z= 0.427 Angle : 0.873 14.208 19961 Z= 0.407 Chirality : 0.062 0.851 2285 Planarity : 0.005 0.036 2055 Dihedral : 17.407 145.307 3044 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.75 % Allowed : 13.14 % Favored : 85.11 % 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: 0.84 (0.23), residues: 1330 helix: 1.33 (0.20), residues: 686 sheet: 0.38 (0.50), residues: 124 loop : -0.35 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 403 TYR 0.022 0.002 TYR B1201 PHE 0.024 0.002 PHE B 98 TRP 0.006 0.002 TRP B 659 HIS 0.009 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.43 (14355) covalent geometry : angle 0.87266 / 0.41 (19961) hydrogen bonds : bond 0.05067 / 2.67 ( 640) hydrogen bonds : angle 4.46517 / 1.83 ( 1756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8342 (mm) REVERT: B 383 MET cc_start: 0.8849 (mtp) cc_final: 0.8624 (mtp) REVERT: B 682 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6841 (t80) REVERT: B 810 LYS cc_start: 0.7857 (mmtp) cc_final: 0.7226 (tttt) REVERT: B 976 ARG cc_start: 0.9117 (mtm-85) cc_final: 0.8697 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8171 (p90) REVERT: B 1242 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6157 (m-10) outliers start: 21 outliers final: 12 residues processed: 58 average time/residue: 0.1189 time to fit residues: 10.4649 Evaluate side-chains 55 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1318 LEU Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057236 restraints weight = 48426.884| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.50 r_work: 0.2964 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14355 Z= 0.126 Angle : 0.625 10.222 19961 Z= 0.299 Chirality : 0.052 0.637 2285 Planarity : 0.003 0.035 2055 Dihedral : 17.198 144.718 3044 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 13.81 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1330 helix: 1.69 (0.20), residues: 679 sheet: 0.41 (0.51), residues: 123 loop : -0.17 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1298 TYR 0.021 0.001 TYR B 882 PHE 0.014 0.001 PHE B 693 TRP 0.008 0.001 TRP B 476 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (14355) covalent geometry : angle 0.62486 / 0.30 (19961) hydrogen bonds : bond 0.03875 / 2.02 ( 640) hydrogen bonds : angle 4.06562 / 1.67 ( 1756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8233 (mm) REVERT: B 353 ASP cc_start: 0.8466 (t70) cc_final: 0.8258 (p0) REVERT: B 383 MET cc_start: 0.8764 (mtp) cc_final: 0.8519 (mtp) REVERT: B 518 PHE cc_start: 0.8326 (t80) cc_final: 0.8107 (t80) REVERT: B 682 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6610 (t80) REVERT: B 810 LYS cc_start: 0.7805 (mmtp) cc_final: 0.7157 (tttt) REVERT: B 976 ARG cc_start: 0.9051 (mtm-85) cc_final: 0.8594 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8057 (p90) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 0.1229 time to fit residues: 10.2606 Evaluate side-chains 52 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 7 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.080854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056146 restraints weight = 48739.669| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.48 r_work: 0.2934 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14355 Z= 0.225 Angle : 0.658 10.822 19961 Z= 0.312 Chirality : 0.052 0.630 2285 Planarity : 0.003 0.035 2055 Dihedral : 17.201 145.930 3044 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.92 % Allowed : 14.23 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1330 helix: 1.67 (0.20), residues: 685 sheet: 0.46 (0.51), residues: 123 loop : -0.19 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 220 TYR 0.020 0.001 TYR B 882 PHE 0.011 0.001 PHE B 518 TRP 0.005 0.001 TRP B 476 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (14355) covalent geometry : angle 0.65774 / 0.31 (19961) hydrogen bonds : bond 0.03994 / 2.10 ( 640) hydrogen bonds : angle 4.08408 / 1.68 ( 1756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8239 (mm) REVERT: B 353 ASP cc_start: 0.8515 (t70) cc_final: 0.8255 (p0) REVERT: B 383 MET cc_start: 0.8823 (mtp) cc_final: 0.8585 (mtp) REVERT: B 682 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6711 (t80) REVERT: B 810 LYS cc_start: 0.7957 (mmtp) cc_final: 0.7266 (tttt) REVERT: B 976 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8629 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8106 (p90) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.1189 time to fit residues: 9.4552 Evaluate side-chains 50 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 141 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.082299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057412 restraints weight = 48496.716| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.54 r_work: 0.2977 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14355 Z= 0.124 Angle : 0.591 9.775 19961 Z= 0.283 Chirality : 0.049 0.560 2285 Planarity : 0.003 0.036 2055 Dihedral : 17.101 145.160 3044 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 13.98 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1330 helix: 1.78 (0.20), residues: 685 sheet: 0.38 (0.50), residues: 123 loop : -0.16 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.021 0.001 TYR B 882 PHE 0.009 0.001 PHE B 518 TRP 0.007 0.001 TRP B 476 HIS 0.006 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14355) covalent geometry : angle 0.59096 / 0.28 (19961) hydrogen bonds : bond 0.03607 / 1.89 ( 640) hydrogen bonds : angle 3.96961 / 1.64 ( 1756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.54 seconds wall clock time: 59 minutes 23.26 seconds (3563.26 seconds total)