Starting phenix.real_space_refine on Sat Jul 4 01:15:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4e_14494/07_2026/7z4e_14494.cif" } resolution = 4.14 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= 0.003 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3728 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 138 5.49 5 S 23 5.16 5 C 8436 2.51 5 N 2467 2.21 5 O 3005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 14069 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 11089 Classifications: {'peptide': 1357} Link IDs: {'PTRANS': 35, 'TRANS': 1321} Chain breaks: 1 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1884 Classifications: {'RNA': 88} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 46, 'rna3p_pyr': 28} Link IDs: {'rna2p': 14, 'rna3p': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Inner-chain residues flagged as termini: ['pdbres=" DT D -3 "'] Classifications: {'DNA': 25} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 24} Time building chain proxies: 3.28, per 1000 atoms: 0.23 Number of scatterers: 14069 At special positions: 0 Unit cell: (94.9, 131.95, 122.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 138 15.00 O 3005 8.00 N 2467 7.00 C 8436 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: 1.38 Conformation dependent library (CDL) restraints added in 522.3 milliseconds 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 53.6% alpha, 8.0% beta 50 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 4.121A pdb=" N ARG B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.664A 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: 3.737A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.737A pdb=" N PHE B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 286 through 303 Processing helix chain 'B' and resid 317 through 343 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.727A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 406 through 410 removed outlier: 4.097A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.269A 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 removed outlier: 3.525A pdb=" N VAL B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 495 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.686A 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 603 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.604A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 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 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 698 Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.450A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 removed outlier: 3.769A pdb=" N HIS B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 803 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.577A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.950A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.766A 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 922 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.950A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.345A 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 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1152 through 1155 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1191 through 1195 Processing helix chain 'B' and resid 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1281 Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 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 sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 3.519A pdb=" N ILE B 43 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 45 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 30 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.541A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.604A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) 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 1049 through 1050 Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'B' and resid 1107 through 1111 removed outlier: 6.668A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1157 through 1167 removed outlier: 3.516A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B1166 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B1196 " --> pdb=" O LEU B1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 517 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 4323 1.35 - 1.50: 4657 1.50 - 1.65: 5599 1.65 - 1.80: 29 1.80 - 1.95: 15 Bond restraints: 14623 Sorted by residual: bond pdb=" SD MET B1021 " pdb=" CE MET B1021 " ideal model delta sigma weight residual 1.791 1.951 -0.160 2.50e-02 1.60e+03 4.10e+01 bond pdb=" CG MET B1021 " pdb=" SD MET B1021 " ideal model delta sigma weight residual 1.803 1.950 -0.147 2.50e-02 1.60e+03 3.46e+01 bond pdb=" C3' DA D -14 " pdb=" C2' DA D -14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 bond pdb=" O3' G A 43 " pdb=" P U A 44 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.51e+00 bond pdb=" N LYS B 163 " pdb=" CA LYS B 163 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.54e+00 ... (remaining 14618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 19582 1.44 - 2.89: 691 2.89 - 4.33: 61 4.33 - 5.78: 5 5.78 - 7.22: 2 Bond angle restraints: 20341 Sorted by residual: angle pdb=" N GLU B 627 " pdb=" CA GLU B 627 " pdb=" C GLU B 627 " ideal model delta sigma weight residual 114.75 107.53 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" O4' DC C 5 " pdb=" C4' DC C 5 " pdb=" C3' DC C 5 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" O4' DT C 4 " pdb=" C4' DT C 4 " pdb=" C3' DT C 4 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT D -9 " pdb=" C4 DT D -9 " pdb=" O4 DT D -9 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 20336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 7811 21.26 - 42.52: 508 42.52 - 63.78: 259 63.78 - 85.04: 10 85.04 - 106.30: 6 Dihedral angle restraints: 8594 sinusoidal: 4604 harmonic: 3990 Sorted by residual: dihedral pdb=" O4' U A 59 " pdb=" C1' U A 59 " pdb=" N1 U A 59 " pdb=" C2 U A 59 " ideal model delta sinusoidal sigma weight residual -128.00 -66.06 -61.94 1 1.70e+01 3.46e-03 1.76e+01 dihedral pdb=" O4' G A 33 " pdb=" C1' G A 33 " pdb=" N9 G A 33 " pdb=" C4 G A 33 " ideal model delta sinusoidal sigma weight residual 70.00 -2.44 72.44 1 2.00e+01 2.50e-03 1.68e+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 -90.00 -33.97 -56.03 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 8591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1735 0.039 - 0.077: 436 0.077 - 0.116: 126 0.116 - 0.155: 16 0.155 - 0.194: 6 Chirality restraints: 2319 Sorted by residual: chirality pdb=" C1' U A 23 " pdb=" O4' U A 23 " pdb=" C2' U A 23 " pdb=" N1 U A 23 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" C1' U A 66 " pdb=" O4' U A 66 " pdb=" C2' U A 66 " pdb=" N1 U A 66 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" C3' C A 20 " pdb=" C4' C A 20 " pdb=" O3' C A 20 " pdb=" C2' C A 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.64 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2316 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 21 " -0.009 2.00e-02 2.50e+03 1.41e-02 5.97e+00 pdb=" N9 G A 21 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 21 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G A 21 " 0.018 2.00e-02 2.50e+03 pdb=" C5 G A 21 " -0.008 2.00e-02 2.50e+03 pdb=" C6 G A 21 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G A 21 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G A 21 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 21 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G A 21 " 0.030 2.00e-02 2.50e+03 pdb=" N3 G A 21 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G A 21 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 20 " -0.024 2.00e-02 2.50e+03 1.47e-02 4.85e+00 pdb=" N1 C A 20 " 0.004 2.00e-02 2.50e+03 pdb=" C2 C A 20 " 0.014 2.00e-02 2.50e+03 pdb=" O2 C A 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C A 20 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C A 20 " 0.014 2.00e-02 2.50e+03 pdb=" N4 C A 20 " -0.028 2.00e-02 2.50e+03 pdb=" C5 C A 20 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A 20 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 24 " -0.023 2.00e-02 2.50e+03 1.30e-02 3.83e+00 pdb=" N1 U A 24 " 0.031 2.00e-02 2.50e+03 pdb=" C2 U A 24 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A 24 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A 24 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U A 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U A 24 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 24 " 0.003 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1078 2.74 - 3.28: 13990 3.28 - 3.82: 25029 3.82 - 4.36: 29663 4.36 - 4.90: 45961 Nonbonded interactions: 115721 Sorted by model distance: nonbonded pdb=" O2' U A 59 " pdb=" OP1 C A 60 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP B1267 " pdb=" OH TYR B1294 " model vdw 2.217 3.040 nonbonded pdb=" O ALA B1227 " pdb=" N2 G A 89 " model vdw 2.241 3.120 nonbonded pdb=" O2' U A 56 " pdb=" N2 G A 58 " model vdw 2.243 3.120 nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.252 3.040 ... (remaining 115716 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 group one per residue 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 0.160 14623 Z= 0.282 Angle : 0.582 7.220 20341 Z= 0.411 Chirality : 0.039 0.194 2319 Planarity : 0.003 0.044 2088 Dihedral : 15.881 106.299 6014 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.64 % Allowed : 5.02 % Favored : 93.34 % 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: 0.67 (0.23), residues: 1353 helix: 1.29 (0.21), residues: 667 sheet: -0.28 (0.50), residues: 111 loop : -0.33 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.007 0.001 TYR B1141 PHE 0.006 0.001 PHE B 97 TRP 0.005 0.001 TRP B 464 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.28 (14623) covalent geometry : angle 0.58165 / 0.41 (20341) hydrogen bonds : bond 0.14878 / 9.52 ( 640) hydrogen bonds : angle 5.74630 / 3.97 ( 1727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8124 (t0) REVERT: B 139 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8218 (mtp180) REVERT: B 415 HIS cc_start: 0.8890 (m90) cc_final: 0.8268 (m-70) REVERT: B 419 LEU cc_start: 0.9571 (tt) cc_final: 0.9349 (pp) REVERT: B 534 MET cc_start: 0.4961 (mtp) cc_final: 0.3639 (ttp) REVERT: B 659 TRP cc_start: 0.7501 (m100) cc_final: 0.6816 (m100) REVERT: B 822 MET cc_start: 0.9514 (tpt) cc_final: 0.9082 (tpp) REVERT: B 848 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4142 (mptt) REVERT: B 856 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.8813 (t) REVERT: B 958 LEU cc_start: 0.9125 (mt) cc_final: 0.8606 (mt) REVERT: B 966 PHE cc_start: 0.9123 (t80) cc_final: 0.8680 (t80) REVERT: B 1213 MET cc_start: 0.7729 (mtm) cc_final: 0.6895 (ttm) REVERT: B 1219 GLU cc_start: 0.8722 (tt0) cc_final: 0.8451 (tm-30) REVERT: B 1355 LEU cc_start: 0.8630 (mt) cc_final: 0.8318 (mt) outliers start: 20 outliers final: 5 residues processed: 213 average time/residue: 0.1442 time to fit residues: 42.7725 Evaluate side-chains 108 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 overall best weight: 3.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 341 GLN B 369 GLN B 412 HIS B 415 HIS B 459 ASN ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 GLN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.061389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.046501 restraints weight = 104272.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047865 restraints weight = 53912.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.048733 restraints weight = 35872.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.049244 restraints weight = 27476.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.049617 restraints weight = 23473.384| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14623 Z= 0.179 Angle : 0.581 7.982 20341 Z= 0.319 Chirality : 0.038 0.171 2319 Planarity : 0.004 0.052 2088 Dihedral : 18.091 107.825 3131 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.16 % Allowed : 1.73 % Favored : 98.11 % 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: 0.86 (0.23), residues: 1353 helix: 1.37 (0.20), residues: 680 sheet: 0.02 (0.49), residues: 110 loop : -0.21 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.012 0.002 TYR B 529 PHE 0.026 0.001 PHE B1313 TRP 0.007 0.001 TRP B 464 HIS 0.005 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (14623) covalent geometry : angle 0.58119 / 0.32 (20341) hydrogen bonds : bond 0.04980 / 3.35 ( 640) hydrogen bonds : angle 4.68327 / 3.23 ( 1727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 MET cc_start: 0.2220 (mtp) cc_final: 0.1215 (ptp) REVERT: B 631 MET cc_start: 0.9432 (mmp) cc_final: 0.9194 (mmt) REVERT: B 659 TRP cc_start: 0.7833 (m100) cc_final: 0.7444 (m100) REVERT: B 727 LEU cc_start: 0.9121 (mt) cc_final: 0.8886 (mt) REVERT: B 781 MET cc_start: 0.8519 (mmm) cc_final: 0.8208 (mmm) REVERT: B 822 MET cc_start: 0.9547 (tpt) cc_final: 0.9196 (tpp) REVERT: B 935 LEU cc_start: 0.9487 (mm) cc_final: 0.9268 (mm) REVERT: B 966 PHE cc_start: 0.9203 (t80) cc_final: 0.8774 (t80) REVERT: B 1046 PHE cc_start: 0.7709 (m-10) cc_final: 0.7275 (m-80) REVERT: B 1213 MET cc_start: 0.7750 (mtm) cc_final: 0.7233 (ttm) REVERT: B 1219 GLU cc_start: 0.8908 (tt0) cc_final: 0.8372 (tm-30) REVERT: B 1350 GLN cc_start: 0.8755 (mt0) cc_final: 0.8473 (mm-40) outliers start: 2 outliers final: 0 residues processed: 120 average time/residue: 0.1161 time to fit residues: 20.6320 Evaluate side-chains 82 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 118 optimal weight: 0.3980 chunk 110 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 53 optimal weight: 0.0070 chunk 137 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.063818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.048494 restraints weight = 116660.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.049992 restraints weight = 58881.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050830 restraints weight = 38377.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051378 restraints weight = 29756.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.051711 restraints weight = 25464.370| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14623 Z= 0.115 Angle : 0.510 9.533 20341 Z= 0.280 Chirality : 0.036 0.169 2319 Planarity : 0.004 0.047 2088 Dihedral : 17.871 106.536 3131 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.08 % Allowed : 1.73 % Favored : 98.19 % 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: 0.96 (0.23), residues: 1353 helix: 1.46 (0.20), residues: 680 sheet: -0.07 (0.48), residues: 110 loop : -0.14 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 139 TYR 0.022 0.001 TYR B1336 PHE 0.018 0.001 PHE B1313 TRP 0.009 0.001 TRP B 18 HIS 0.006 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (14623) covalent geometry : angle 0.51020 / 0.28 (20341) hydrogen bonds : bond 0.03811 / 2.51 ( 640) hydrogen bonds : angle 4.39373 / 3.03 ( 1727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8877 (mmp) cc_final: 0.8520 (tpp) REVERT: B 383 MET cc_start: 0.8678 (mmp) cc_final: 0.8176 (mmm) REVERT: B 534 MET cc_start: 0.3776 (mtp) cc_final: 0.2705 (ptp) REVERT: B 631 MET cc_start: 0.9415 (mmp) cc_final: 0.9187 (mmt) REVERT: B 659 TRP cc_start: 0.7675 (m100) cc_final: 0.7174 (m100) REVERT: B 718 ASP cc_start: 0.9287 (m-30) cc_final: 0.8755 (p0) REVERT: B 781 MET cc_start: 0.8762 (mmm) cc_final: 0.8479 (mmm) REVERT: B 822 MET cc_start: 0.9554 (tpt) cc_final: 0.9165 (tpp) REVERT: B 966 PHE cc_start: 0.9225 (t80) cc_final: 0.9009 (t80) REVERT: B 1197 LYS cc_start: 0.9218 (mtpp) cc_final: 0.8923 (tttm) REVERT: B 1213 MET cc_start: 0.7677 (mtm) cc_final: 0.7415 (ttm) REVERT: B 1350 GLN cc_start: 0.8883 (mt0) cc_final: 0.8595 (mm-40) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1076 time to fit residues: 17.7274 Evaluate side-chains 75 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 9 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.061396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.046103 restraints weight = 121219.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047523 restraints weight = 61271.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.048317 restraints weight = 40417.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.048840 restraints weight = 31590.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.049182 restraints weight = 27155.433| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14623 Z= 0.181 Angle : 0.534 5.937 20341 Z= 0.293 Chirality : 0.036 0.151 2319 Planarity : 0.004 0.045 2088 Dihedral : 17.901 107.861 3131 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.13 (0.23), residues: 1353 helix: 1.68 (0.20), residues: 675 sheet: -0.27 (0.50), residues: 107 loop : -0.10 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.017 0.001 TYR B 136 PHE 0.016 0.001 PHE B1008 TRP 0.013 0.001 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (14623) covalent geometry : angle 0.53382 / 0.29 (20341) hydrogen bonds : bond 0.04723 / 3.18 ( 640) hydrogen bonds : angle 4.51710 / 3.12 ( 1727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8702 (mmp) cc_final: 0.8184 (mmm) REVERT: B 534 MET cc_start: 0.4391 (mtp) cc_final: 0.3382 (ptp) REVERT: B 631 MET cc_start: 0.9426 (mmp) cc_final: 0.9221 (mmt) REVERT: B 659 TRP cc_start: 0.7769 (m100) cc_final: 0.7257 (m100) REVERT: B 718 ASP cc_start: 0.9294 (m-30) cc_final: 0.8762 (p0) REVERT: B 740 THR cc_start: 0.8854 (m) cc_final: 0.8591 (m) REVERT: B 780 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8594 (mtm-85) REVERT: B 781 MET cc_start: 0.8910 (mmm) cc_final: 0.8310 (mmm) REVERT: B 822 MET cc_start: 0.9590 (tpt) cc_final: 0.9256 (tpp) REVERT: B 1213 MET cc_start: 0.8011 (mtm) cc_final: 0.7343 (ttm) REVERT: B 1219 GLU cc_start: 0.8950 (tt0) cc_final: 0.8448 (tm-30) REVERT: B 1242 TYR cc_start: 0.7584 (t80) cc_final: 0.7239 (t80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1021 time to fit residues: 15.2426 Evaluate side-chains 73 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 145 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN B 459 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.058310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043155 restraints weight = 109587.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.044501 restraints weight = 58294.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.045247 restraints weight = 39241.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045744 restraints weight = 30994.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046066 restraints weight = 26682.878| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.004 0.047 14623 Z= 0.190 Angle : 0.555 8.095 20341 Z= 0.299 Chirality : 0.037 0.152 2319 Planarity : 0.004 0.046 2088 Dihedral : 18.008 107.857 3131 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.08 % Allowed : 1.23 % Favored : 98.68 % 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: 1353 helix: 1.65 (0.20), residues: 677 sheet: 0.22 (0.56), residues: 87 loop : -0.18 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 586 TYR 0.018 0.002 TYR B 373 PHE 0.019 0.002 PHE B 32 TRP 0.022 0.002 TRP B 18 HIS 0.009 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (14623) covalent geometry : angle 0.55453 / 0.30 (20341) hydrogen bonds : bond 0.04683 / 3.14 ( 640) hydrogen bonds : angle 4.52140 / 3.12 ( 1727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8659 (mmp) cc_final: 0.8116 (mmm) REVERT: B 459 ASN cc_start: 0.4768 (OUTLIER) cc_final: 0.4432 (t0) REVERT: B 534 MET cc_start: 0.3492 (mtp) cc_final: 0.2757 (ptp) REVERT: B 631 MET cc_start: 0.9432 (mmp) cc_final: 0.9221 (mmt) REVERT: B 659 TRP cc_start: 0.8094 (m100) cc_final: 0.7573 (m100) REVERT: B 718 ASP cc_start: 0.9267 (m-30) cc_final: 0.8755 (p0) REVERT: B 740 THR cc_start: 0.8878 (m) cc_final: 0.8665 (m) REVERT: B 780 ARG cc_start: 0.9131 (mtt180) cc_final: 0.8639 (mtm-85) REVERT: B 781 MET cc_start: 0.9071 (mmm) cc_final: 0.8380 (mmm) REVERT: B 822 MET cc_start: 0.9575 (tpt) cc_final: 0.8688 (tpp) REVERT: B 823 TYR cc_start: 0.7794 (m-10) cc_final: 0.7423 (m-10) REVERT: B 1213 MET cc_start: 0.8004 (mtm) cc_final: 0.7339 (ttm) REVERT: B 1242 TYR cc_start: 0.7564 (t80) cc_final: 0.7228 (t80) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0980 time to fit residues: 14.6811 Evaluate side-chains 70 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 89 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.056266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.041515 restraints weight = 113566.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.042786 restraints weight = 60665.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.043491 restraints weight = 40935.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.043999 restraints weight = 32384.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.044294 restraints weight = 27800.542| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.005 0.063 14623 Z= 0.266 Angle : 0.637 7.265 20341 Z= 0.343 Chirality : 0.039 0.177 2319 Planarity : 0.005 0.048 2088 Dihedral : 18.285 109.239 3131 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.78 (0.23), residues: 1353 helix: 1.42 (0.20), residues: 679 sheet: -0.18 (0.56), residues: 87 loop : -0.39 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 139 TYR 0.019 0.002 TYR B 136 PHE 0.020 0.002 PHE B 375 TRP 0.033 0.003 TRP B 464 HIS 0.012 0.002 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.27 (14623) covalent geometry : angle 0.63713 / 0.34 (20341) hydrogen bonds : bond 0.06384 / 4.34 ( 640) hydrogen bonds : angle 4.80753 / 3.33 ( 1727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8671 (mmp) cc_final: 0.8154 (mmm) REVERT: B 534 MET cc_start: 0.3447 (mtp) cc_final: 0.2815 (ptp) REVERT: B 718 ASP cc_start: 0.9287 (m-30) cc_final: 0.8812 (p0) REVERT: B 740 THR cc_start: 0.8944 (m) cc_final: 0.8675 (p) REVERT: B 780 ARG cc_start: 0.9101 (mtt180) cc_final: 0.8557 (mtm-85) REVERT: B 781 MET cc_start: 0.9156 (mmm) cc_final: 0.8456 (mmm) REVERT: B 822 MET cc_start: 0.9504 (tpt) cc_final: 0.9034 (tpp) REVERT: B 1213 MET cc_start: 0.8015 (mtm) cc_final: 0.7343 (ttm) REVERT: B 1219 GLU cc_start: 0.8949 (tt0) cc_final: 0.8551 (tt0) REVERT: B 1242 TYR cc_start: 0.7830 (t80) cc_final: 0.7460 (t80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1030 time to fit residues: 14.7922 Evaluate side-chains 65 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 64 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 145 optimal weight: 50.0000 chunk 26 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 511 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.055443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039777 restraints weight = 120192.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040997 restraints weight = 66612.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.041764 restraints weight = 46491.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042219 restraints weight = 37311.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.042452 restraints weight = 32650.044| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14623 Z= 0.267 Angle : 0.641 10.667 20341 Z= 0.343 Chirality : 0.039 0.193 2319 Planarity : 0.004 0.049 2088 Dihedral : 18.449 108.713 3131 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 0.67 (0.23), residues: 1353 helix: 1.35 (0.20), residues: 678 sheet: -0.31 (0.58), residues: 82 loop : -0.44 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 78 TYR 0.023 0.002 TYR B 823 PHE 0.025 0.002 PHE B 966 TRP 0.025 0.003 TRP B 464 HIS 0.006 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.27 (14623) covalent geometry : angle 0.64087 / 0.34 (20341) hydrogen bonds : bond 0.05760 / 3.91 ( 640) hydrogen bonds : angle 4.84336 / 3.37 ( 1727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8683 (mmp) cc_final: 0.8150 (mmm) REVERT: B 534 MET cc_start: 0.4087 (mtp) cc_final: 0.3379 (ptp) REVERT: B 631 MET cc_start: 0.9318 (mmt) cc_final: 0.9081 (mmm) REVERT: B 718 ASP cc_start: 0.9377 (m-30) cc_final: 0.8884 (p0) REVERT: B 780 ARG cc_start: 0.8978 (mtt180) cc_final: 0.8482 (mtm-85) REVERT: B 781 MET cc_start: 0.9179 (mmm) cc_final: 0.8479 (mmm) REVERT: B 822 MET cc_start: 0.9483 (tpt) cc_final: 0.9181 (tpp) REVERT: B 1213 MET cc_start: 0.7983 (mtm) cc_final: 0.7305 (ttm) REVERT: B 1219 GLU cc_start: 0.8974 (tt0) cc_final: 0.8557 (tt0) REVERT: B 1242 TYR cc_start: 0.8034 (t80) cc_final: 0.7656 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0966 time to fit residues: 13.1382 Evaluate side-chains 64 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 135 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 145 optimal weight: 50.0000 chunk 117 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 54 optimal weight: 50.0000 chunk 125 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 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 = 0.3572 r_free = 0.3572 target = 0.056018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040630 restraints weight = 119267.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041834 restraints weight = 65617.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042615 restraints weight = 45469.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.043028 restraints weight = 36469.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.043322 restraints weight = 32011.551| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14623 Z= 0.187 Angle : 0.570 8.669 20341 Z= 0.308 Chirality : 0.037 0.157 2319 Planarity : 0.004 0.047 2088 Dihedral : 18.368 107.511 3131 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.23), residues: 1353 helix: 1.49 (0.20), residues: 676 sheet: -0.27 (0.57), residues: 82 loop : -0.39 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.030 0.002 TYR B 5 PHE 0.019 0.002 PHE B 970 TRP 0.035 0.003 TRP B 659 HIS 0.013 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (14623) covalent geometry : angle 0.57041 / 0.31 (20341) hydrogen bonds : bond 0.04872 / 3.29 ( 640) hydrogen bonds : angle 4.74759 / 3.31 ( 1727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8687 (mmp) cc_final: 0.8104 (mmm) REVERT: B 450 TYR cc_start: 0.6804 (m-80) cc_final: 0.6430 (m-80) REVERT: B 534 MET cc_start: 0.4035 (mtp) cc_final: 0.3416 (ptp) REVERT: B 631 MET cc_start: 0.9340 (mmt) cc_final: 0.9092 (mmm) REVERT: B 718 ASP cc_start: 0.9376 (m-30) cc_final: 0.8885 (p0) REVERT: B 740 THR cc_start: 0.8908 (m) cc_final: 0.8701 (p) REVERT: B 780 ARG cc_start: 0.9008 (mtt180) cc_final: 0.8494 (mtm-85) REVERT: B 781 MET cc_start: 0.9205 (mmm) cc_final: 0.8509 (mmm) REVERT: B 1213 MET cc_start: 0.7927 (mtm) cc_final: 0.7279 (ttm) REVERT: B 1219 GLU cc_start: 0.8950 (tt0) cc_final: 0.8549 (tt0) REVERT: B 1242 TYR cc_start: 0.7896 (t80) cc_final: 0.7534 (t80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1015 time to fit residues: 14.0453 Evaluate side-chains 64 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 85 optimal weight: 50.0000 chunk 124 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 68 optimal weight: 40.0000 chunk 107 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.055434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.040082 restraints weight = 120794.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.041324 restraints weight = 66325.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.042000 restraints weight = 45730.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042484 restraints weight = 36763.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042825 restraints weight = 32070.706| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14623 Z= 0.226 Angle : 0.599 8.965 20341 Z= 0.322 Chirality : 0.038 0.166 2319 Planarity : 0.004 0.048 2088 Dihedral : 18.380 107.623 3131 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.77 (0.23), residues: 1353 helix: 1.41 (0.20), residues: 677 sheet: -0.23 (0.57), residues: 82 loop : -0.38 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 78 TYR 0.026 0.002 TYR B1265 PHE 0.019 0.002 PHE B 375 TRP 0.021 0.002 TRP B 464 HIS 0.006 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (14623) covalent geometry : angle 0.59897 / 0.32 (20341) hydrogen bonds : bond 0.05391 / 3.66 ( 640) hydrogen bonds : angle 4.81154 / 3.35 ( 1727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8695 (mmp) cc_final: 0.8089 (mmm) REVERT: B 450 TYR cc_start: 0.6835 (m-80) cc_final: 0.6466 (m-80) REVERT: B 534 MET cc_start: 0.3967 (mtp) cc_final: 0.3386 (ptp) REVERT: B 631 MET cc_start: 0.9342 (mmt) cc_final: 0.9107 (mmm) REVERT: B 718 ASP cc_start: 0.9371 (m-30) cc_final: 0.8866 (p0) REVERT: B 740 THR cc_start: 0.8950 (m) cc_final: 0.8728 (p) REVERT: B 780 ARG cc_start: 0.9013 (mtt180) cc_final: 0.8487 (mtm-85) REVERT: B 781 MET cc_start: 0.9230 (mmm) cc_final: 0.8592 (mmm) REVERT: B 822 MET cc_start: 0.9271 (mmp) cc_final: 0.8573 (mmm) REVERT: B 1169 MET cc_start: 0.8753 (mmt) cc_final: 0.8217 (mmm) REVERT: B 1213 MET cc_start: 0.7939 (mtm) cc_final: 0.7677 (mtt) REVERT: B 1219 GLU cc_start: 0.8953 (tt0) cc_final: 0.8561 (tt0) REVERT: B 1242 TYR cc_start: 0.7976 (t80) cc_final: 0.7612 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0995 time to fit residues: 13.1190 Evaluate side-chains 62 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 61 optimal weight: 40.0000 chunk 21 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.057619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.042150 restraints weight = 117251.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.043447 restraints weight = 64249.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.044194 restraints weight = 44040.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.044695 restraints weight = 35204.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.045026 restraints weight = 30613.261| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14623 Z= 0.111 Angle : 0.533 9.816 20341 Z= 0.283 Chirality : 0.037 0.158 2319 Planarity : 0.003 0.044 2088 Dihedral : 18.065 104.278 3131 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.08 % Allowed : 0.00 % Favored : 99.92 % 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: 1.06 (0.23), residues: 1353 helix: 1.66 (0.20), residues: 676 sheet: -0.31 (0.55), residues: 82 loop : -0.20 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.017 0.001 TYR B1265 PHE 0.012 0.001 PHE B1258 TRP 0.012 0.002 TRP B 18 HIS 0.005 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (14623) covalent geometry : angle 0.53320 / 0.28 (20341) hydrogen bonds : bond 0.03619 / 2.38 ( 640) hydrogen bonds : angle 4.42990 / 3.06 ( 1727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 LEU cc_start: 0.9212 (pp) cc_final: 0.8795 (mp) REVERT: B 383 MET cc_start: 0.8661 (mmp) cc_final: 0.8367 (tpp) REVERT: B 450 TYR cc_start: 0.6713 (m-80) cc_final: 0.6369 (m-10) REVERT: B 534 MET cc_start: 0.3859 (mtp) cc_final: 0.3332 (ptp) REVERT: B 631 MET cc_start: 0.9352 (mmt) cc_final: 0.9081 (mmm) REVERT: B 718 ASP cc_start: 0.9358 (m-30) cc_final: 0.8818 (p0) REVERT: B 722 GLU cc_start: 0.9483 (mp0) cc_final: 0.9009 (mp0) REVERT: B 740 THR cc_start: 0.8846 (m) cc_final: 0.8640 (p) REVERT: B 780 ARG cc_start: 0.9002 (mtt180) cc_final: 0.8505 (mtm-85) REVERT: B 781 MET cc_start: 0.9226 (mmm) cc_final: 0.8554 (mmm) REVERT: B 822 MET cc_start: 0.9191 (mmp) cc_final: 0.8604 (mmm) REVERT: B 1043 MET cc_start: 0.9216 (tpt) cc_final: 0.9006 (tpt) REVERT: B 1169 MET cc_start: 0.8792 (mmt) cc_final: 0.8241 (mmm) REVERT: B 1219 GLU cc_start: 0.8870 (tt0) cc_final: 0.8511 (tt0) REVERT: B 1242 TYR cc_start: 0.7822 (t80) cc_final: 0.7457 (t80) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1053 time to fit residues: 15.4502 Evaluate side-chains 66 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 17 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 89 optimal weight: 0.0970 overall best weight: 2.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.056785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.041409 restraints weight = 118354.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042692 restraints weight = 65116.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.043418 restraints weight = 44743.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.043892 restraints weight = 35799.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.044164 restraints weight = 31211.916| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14623 Z= 0.147 Angle : 0.551 12.516 20341 Z= 0.294 Chirality : 0.037 0.169 2319 Planarity : 0.003 0.044 2088 Dihedral : 17.975 105.003 3131 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: 1.06 (0.23), residues: 1353 helix: 1.67 (0.20), residues: 678 sheet: -0.18 (0.57), residues: 82 loop : -0.24 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.018 0.001 TYR B1265 PHE 0.018 0.001 PHE B 98 TRP 0.012 0.002 TRP B 464 HIS 0.005 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (14623) covalent geometry : angle 0.55081 / 0.29 (20341) hydrogen bonds : bond 0.04179 / 2.80 ( 640) hydrogen bonds : angle 4.47289 / 3.09 ( 1727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.60 seconds wall clock time: 42 minutes 34.21 seconds (2554.21 seconds total)