Starting phenix.real_space_refine on Fri Jul 3 12:24:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4i_14498/07_2026/7z4i_14498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4i_14498/07_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_14498/07_2026/7z4i_14498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4i_14498/07_2026/7z4i_14498.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4i_14498/07_2026/7z4i_14498.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4i_14498/07_2026/7z4i_14498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4i_14498/07_2026/7z4i_14498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4i_14498/07_2026/7z4i_14498.map" } 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-dev-6108/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: {'RNA': 96} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 83} 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: 2.16, per 1000 atoms: 0.16 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: 1.01 Conformation dependent library (CDL) restraints added in 467.6 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: 1.78 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: 2.82 Time building geometry restraints manager: 1.33 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: 19214 1.12 - 2.25: 579 2.25 - 3.37: 149 3.37 - 4.49: 14 4.49 - 5.62: 5 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: 7935 27.05 - 54.10: 421 54.10 - 81.15: 76 81.15 - 108.20: 4 108.20 - 135.25: 1 Dihedral angle restraints: 8437 sinusoidal: 4500 harmonic: 3937 Sorted by residual: dihedral pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " pdb=" P DA C 17 " ideal model delta sinusoidal sigma weight residual 220.00 84.75 135.25 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" O4' G A 82 " pdb=" C1' G A 82 " pdb=" N9 G A 82 " pdb=" C4 G A 82 " ideal model delta sinusoidal sigma weight residual 70.00 11.76 58.24 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ILE B 300 " pdb=" C ILE B 300 " pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1703 0.036 - 0.073: 435 0.073 - 0.109: 106 0.109 - 0.145: 37 0.145 - 0.182: 4 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CA ASN B 77 " pdb=" N ASN B 77 " pdb=" C ASN B 77 " pdb=" CB ASN B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" C3' DT C 11 " pdb=" C4' DT C 11 " pdb=" O3' DT C 11 " pdb=" C2' DT C 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" C1' A A 35 " pdb=" O4' A A 35 " pdb=" C2' A A 35 " pdb=" N9 A A 35 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.87e-01 ... (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: 3.610 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- 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= 0.272 Angle : 0.496 5.617 19961 Z= 0.341 Chirality : 0.038 0.182 2285 Planarity : 0.004 0.044 2055 Dihedral : 15.112 135.253 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 0.00363 / 0.27 (14355) covalent geometry : angle 0.49639 / 0.34 (19961) hydrogen bonds : bond 0.12956 / 7.51 ( 640) hydrogen bonds : angle 5.33417 / 3.03 ( 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 : 0.503 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: 0.1699 time to fit residues: 30.9492 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 : 0.483 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.085467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.060773 restraints weight = 48737.720| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.48 r_work: 0.3066 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14355 Z= 0.160 Angle : 0.519 7.591 19961 Z= 0.284 Chirality : 0.038 0.147 2285 Planarity : 0.004 0.051 2055 Dihedral : 14.700 134.330 3047 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 1.12 (0.23), residues: 1330 helix: 1.50 (0.20), residues: 685 sheet: 0.01 (0.47), residues: 126 loop : 0.03 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 215 TYR 0.021 0.001 TYR B1010 PHE 0.013 0.001 PHE B 196 TRP 0.003 0.001 TRP B 464 HIS 0.008 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (14355) covalent geometry : angle 0.51921 / 0.28 (19961) hydrogen bonds : bond 0.04352 / 2.54 ( 640) hydrogen bonds : angle 4.38855 / 2.44 ( 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 : 0.489 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: 0.8084 (mm-30) cc_final: 0.7563 (tp30) REVERT: B 495 MET cc_start: 0.9025 (mtm) cc_final: 0.8821 (mtt) REVERT: B 610 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8187 (tp30) REVERT: B 810 LYS cc_start: 0.7481 (mmtp) cc_final: 0.6806 (tttt) REVERT: B 882 TYR cc_start: 0.7232 (t80) cc_final: 0.6747 (t80) REVERT: B 911 LEU cc_start: 0.9607 (mt) cc_final: 0.9396 (tp) REVERT: B 933 GLN cc_start: 0.9289 (tt0) cc_final: 0.8818 (tm-30) REVERT: B 1037 PHE cc_start: 0.8578 (p90) cc_final: 0.7988 (p90) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.1644 time to fit residues: 16.2970 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 : 0.474 ------------------------------------------------------------------------------- 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: 10.0000 chunk 96 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 511 HIS B 712 GLN B 826 GLN B 885 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.081537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056613 restraints weight = 49193.070| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.48 r_work: 0.2938 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 14355 Z= 0.342 Angle : 0.668 9.710 19961 Z= 0.352 Chirality : 0.042 0.170 2285 Planarity : 0.004 0.045 2055 Dihedral : 14.992 134.404 3045 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.58 % Allowed : 10.32 % Favored : 88.10 % 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: 0.92 (0.23), residues: 1330 helix: 1.38 (0.20), residues: 678 sheet: 0.12 (0.50), residues: 126 loop : -0.18 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 919 TYR 0.055 0.002 TYR B1039 PHE 0.023 0.002 PHE B1008 TRP 0.005 0.001 TRP B 18 HIS 0.007 0.002 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.34 (14355) covalent geometry : angle 0.66810 / 0.35 (19961) hydrogen bonds : bond 0.04795 / 2.83 ( 640) hydrogen bonds : angle 4.44684 / 2.49 ( 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 68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 610 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8433 (tp30) REVERT: B 810 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7110 (tttt) REVERT: B 882 TYR cc_start: 0.7083 (t80) cc_final: 0.6783 (t80) REVERT: B 933 GLN cc_start: 0.9353 (tt0) cc_final: 0.8873 (tm-30) REVERT: B 1037 PHE cc_start: 0.8544 (p90) cc_final: 0.7822 (p90) REVERT: B 1273 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8998 (mp) outliers start: 19 outliers final: 11 residues processed: 66 average time/residue: 0.1231 time to fit residues: 12.1084 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 : 0.505 ------------------------------------------------------------------------------- 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: 2.9990 chunk 116 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.083604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058493 restraints weight = 48787.840| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.52 r_work: 0.2996 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14355 Z= 0.119 Angle : 0.477 6.146 19961 Z= 0.261 Chirality : 0.037 0.141 2285 Planarity : 0.003 0.039 2055 Dihedral : 14.793 134.005 3045 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.25 % Allowed : 11.06 % 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: 1.27 (0.23), residues: 1330 helix: 1.71 (0.20), residues: 678 sheet: 0.14 (0.49), residues: 126 loop : -0.03 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 215 TYR 0.017 0.001 TYR B 155 PHE 0.009 0.001 PHE B1313 TRP 0.009 0.001 TRP B 883 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (14355) covalent geometry : angle 0.47700 / 0.26 (19961) hydrogen bonds : bond 0.03784 / 2.23 ( 640) hydrogen bonds : angle 4.11220 / 2.31 ( 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 60 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 610 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8337 (tp30) REVERT: B 810 LYS cc_start: 0.7693 (mmtp) cc_final: 0.7022 (tttt) REVERT: B 1037 PHE cc_start: 0.8503 (p90) cc_final: 0.7982 (p90) outliers start: 15 outliers final: 7 residues processed: 59 average time/residue: 0.1297 time to fit residues: 11.3709 Evaluate side-chains 48 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 30 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.080801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055678 restraints weight = 48936.816| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.47 r_work: 0.2922 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14355 Z= 0.302 Angle : 0.605 7.700 19961 Z= 0.322 Chirality : 0.040 0.164 2285 Planarity : 0.004 0.043 2055 Dihedral : 14.875 134.613 3044 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.58 % Allowed : 10.98 % Favored : 87.44 % 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: 1.10 (0.23), residues: 1330 helix: 1.55 (0.20), residues: 679 sheet: 0.23 (0.50), residues: 126 loop : -0.15 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 586 TYR 0.017 0.002 TYR B 136 PHE 0.016 0.002 PHE B 98 TRP 0.005 0.001 TRP B 18 HIS 0.006 0.002 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.30 (14355) covalent geometry : angle 0.60500 / 0.32 (19961) hydrogen bonds : bond 0.04484 / 2.66 ( 640) hydrogen bonds : angle 4.26909 / 2.39 ( 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 : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 810 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7058 (tttt) REVERT: B 879 MET cc_start: 0.5084 (mtm) cc_final: 0.4873 (mpp) REVERT: B 976 ARG cc_start: 0.8993 (mtm-85) cc_final: 0.8629 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7940 (p90) outliers start: 19 outliers final: 12 residues processed: 58 average time/residue: 0.1216 time to fit residues: 10.7356 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 : 0.326 ------------------------------------------------------------------------------- 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 795 ILE Chi-restraints excluded: chain B residue 949 LEU 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: 0.7980 chunk 98 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 119 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.082958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058191 restraints weight = 47889.014| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.48 r_work: 0.2993 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14355 Z= 0.109 Angle : 0.462 5.450 19961 Z= 0.255 Chirality : 0.036 0.171 2285 Planarity : 0.003 0.039 2055 Dihedral : 14.677 134.405 3044 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.00 % Allowed : 11.90 % Favored : 87.10 % 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: 1.40 (0.23), residues: 1330 helix: 1.86 (0.20), residues: 676 sheet: 0.38 (0.50), residues: 125 loop : -0.10 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1298 TYR 0.018 0.001 TYR B 155 PHE 0.010 0.001 PHE B1313 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 0.00222 / 0.11 (14355) covalent geometry : angle 0.46218 / 0.25 (19961) hydrogen bonds : bond 0.03594 / 2.13 ( 640) hydrogen bonds : angle 4.02302 / 2.28 ( 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 57 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 810 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7049 (tttt) REVERT: B 823 TYR cc_start: 0.6788 (m-80) cc_final: 0.6459 (t80) REVERT: B 976 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.8545 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7992 (p90) outliers start: 12 outliers final: 6 residues processed: 56 average time/residue: 0.1194 time to fit residues: 10.3789 Evaluate side-chains 49 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.080828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055850 restraints weight = 48575.859| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.44 r_work: 0.2924 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14355 Z= 0.258 Angle : 0.540 4.972 19961 Z= 0.290 Chirality : 0.039 0.158 2285 Planarity : 0.003 0.038 2055 Dihedral : 14.802 135.081 3044 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.41 % Allowed : 12.40 % Favored : 86.19 % 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: 1.26 (0.23), residues: 1330 helix: 1.73 (0.20), residues: 679 sheet: 0.35 (0.51), residues: 124 loop : -0.15 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 403 TYR 0.020 0.002 TYR B 882 PHE 0.023 0.001 PHE B 518 TRP 0.005 0.001 TRP B 18 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.26 (14355) covalent geometry : angle 0.54020 / 0.29 (19961) hydrogen bonds : bond 0.04100 / 2.43 ( 640) hydrogen bonds : angle 4.12652 / 2.32 ( 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 60 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8210 (mm) REVERT: B 810 LYS cc_start: 0.7793 (mmtp) cc_final: 0.7102 (tttt) REVERT: B 976 ARG cc_start: 0.9027 (mtm-85) cc_final: 0.8625 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7940 (p90) outliers start: 17 outliers final: 10 residues processed: 57 average time/residue: 0.1219 time to fit residues: 10.5372 Evaluate side-chains 53 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 795 ILE Chi-restraints excluded: chain B residue 949 LEU 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: 6.9990 chunk 92 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 118 optimal weight: 0.0980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.080354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.055285 restraints weight = 48807.462| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.44 r_work: 0.2920 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14355 Z= 0.237 Angle : 0.531 6.619 19961 Z= 0.288 Chirality : 0.038 0.157 2285 Planarity : 0.003 0.035 2055 Dihedral : 14.869 135.068 3044 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.41 % Allowed : 12.98 % Favored : 85.61 % 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: 1.17 (0.23), residues: 1330 helix: 1.63 (0.20), residues: 686 sheet: 0.34 (0.51), residues: 123 loop : -0.19 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1298 TYR 0.021 0.002 TYR B 882 PHE 0.014 0.001 PHE B 518 TRP 0.005 0.001 TRP B 476 HIS 0.006 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (14355) covalent geometry : angle 0.53146 / 0.29 (19961) hydrogen bonds : bond 0.04003 / 2.36 ( 640) hydrogen bonds : angle 4.14210 / 2.34 ( 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 60 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8253 (mm) REVERT: B 810 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7161 (tttt) REVERT: B 823 TYR cc_start: 0.7115 (m-80) cc_final: 0.6758 (t80) REVERT: B 976 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8623 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8075 (p90) REVERT: B 1242 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.5935 (m-10) outliers start: 17 outliers final: 13 residues processed: 57 average time/residue: 0.1185 time to fit residues: 10.0561 Evaluate side-chains 56 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 949 LEU 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 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: 0.8980 chunk 59 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.081875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056840 restraints weight = 48936.941| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.50 r_work: 0.2967 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14355 Z= 0.114 Angle : 0.452 7.685 19961 Z= 0.251 Chirality : 0.036 0.140 2285 Planarity : 0.003 0.036 2055 Dihedral : 14.695 134.681 3044 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.00 % Allowed : 13.48 % Favored : 85.52 % 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: 1.36 (0.23), residues: 1330 helix: 1.82 (0.20), residues: 690 sheet: 0.39 (0.51), residues: 123 loop : -0.15 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1298 TYR 0.020 0.001 TYR B 882 PHE 0.025 0.001 PHE B 518 TRP 0.008 0.001 TRP B 476 HIS 0.006 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (14355) covalent geometry : angle 0.45243 / 0.25 (19961) hydrogen bonds : bond 0.03536 / 2.09 ( 640) hydrogen bonds : angle 3.98247 / 2.27 ( 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 55 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 810 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7143 (tttt) REVERT: B 823 TYR cc_start: 0.7160 (m-80) cc_final: 0.6821 (t80) REVERT: B 1037 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8045 (p90) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.1116 time to fit residues: 9.3895 Evaluate side-chains 49 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 795 ILE Chi-restraints excluded: chain B residue 879 MET 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: 10.0000 chunk 101 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.080863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055872 restraints weight = 49077.553| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.46 r_work: 0.2938 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14355 Z= 0.188 Angle : 0.483 5.659 19961 Z= 0.264 Chirality : 0.037 0.148 2285 Planarity : 0.003 0.038 2055 Dihedral : 14.751 135.366 3044 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.08 % Allowed : 13.73 % Favored : 85.19 % 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: 1.33 (0.23), residues: 1330 helix: 1.79 (0.20), residues: 691 sheet: 0.44 (0.51), residues: 123 loop : -0.19 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1298 TYR 0.020 0.001 TYR B 882 PHE 0.027 0.001 PHE B 518 TRP 0.005 0.001 TRP B 476 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (14355) covalent geometry : angle 0.48301 / 0.26 (19961) hydrogen bonds : bond 0.03757 / 2.23 ( 640) hydrogen bonds : angle 4.00831 / 2.28 ( 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: 13 poor density : 41 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 810 LYS cc_start: 0.7851 (mmtp) cc_final: 0.7192 (tttt) REVERT: B 823 TYR cc_start: 0.7248 (m-80) cc_final: 0.6711 (t80) REVERT: B 879 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.5061 (ptp) REVERT: B 976 ARG cc_start: 0.9023 (mtm-85) cc_final: 0.8597 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8055 (p90) outliers start: 13 outliers final: 9 residues processed: 50 average time/residue: 0.1324 time to fit residues: 9.9758 Evaluate side-chains 52 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 795 ILE Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.081214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056227 restraints weight = 49148.227| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.42 r_work: 0.2947 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14355 Z= 0.158 Angle : 0.470 9.229 19961 Z= 0.258 Chirality : 0.036 0.145 2285 Planarity : 0.003 0.037 2055 Dihedral : 14.732 135.397 3044 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 14.06 % 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: 1.41 (0.23), residues: 1330 helix: 1.88 (0.20), residues: 685 sheet: 0.43 (0.51), residues: 123 loop : -0.15 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 535 TYR 0.021 0.001 TYR B 882 PHE 0.022 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 0.00338 / 0.16 (14355) covalent geometry : angle 0.47031 / 0.26 (19961) hydrogen bonds : bond 0.03612 / 2.14 ( 640) hydrogen bonds : angle 3.98636 / 2.27 ( 1756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.46 seconds wall clock time: 58 minutes 17.00 seconds (3497.00 seconds total)