Starting phenix.real_space_refine on Sat Sep 12 17:55:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4e_14494/09_2026/7z4e_14494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4e_14494/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z4e_14494/09_2026/7z4e_14494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4e_14494/09_2026/7z4e_14494.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4e_14494/09_2026/7z4e_14494.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4e_14494/09_2026/7z4e_14494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4e_14494/09_2026/7z4e_14494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4e_14494/09_2026/7z4e_14494.map" } 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): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 46, 'rna3p_pyr': 28} Link IDs: {'rna2p': 14, 'rna3p': 73} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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: 2.92, per 1000 atoms: 0.21 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: 1.12 Conformation dependent library (CDL) restraints added in 472.1 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: 1.75 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: 3.10 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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=" O3' G A 43 " pdb=" P U A 44 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.33e+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=" 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: 19331 1.44 - 2.89: 824 2.89 - 4.33: 152 4.33 - 5.78: 32 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 - 17.81: 7502 17.81 - 35.62: 586 35.62 - 53.43: 333 53.43 - 71.24: 157 71.24 - 89.05: 16 Dihedral angle restraints: 8594 sinusoidal: 4604 harmonic: 3990 Sorted by residual: dihedral pdb=" C4' U A 63 " pdb=" C3' U A 63 " pdb=" C2' U A 63 " pdb=" C1' U A 63 " ideal model delta sinusoidal sigma weight residual 36.35 -38.34 74.68 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" C4' C A 67 " pdb=" C3' C A 67 " pdb=" C2' C A 67 " pdb=" C1' C A 67 " ideal model delta sinusoidal sigma weight residual 36.35 -38.34 74.68 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" C4' G A 43 " pdb=" C3' G A 43 " pdb=" C2' G A 43 " pdb=" C1' G A 43 " ideal model delta sinusoidal sigma weight residual 36.34 -37.38 73.73 1 3.10e+00 1.04e-01 7.19e+02 ... (remaining 8591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1958 0.062 - 0.124: 233 0.124 - 0.186: 18 0.186 - 0.248: 70 0.248 - 0.310: 40 Chirality restraints: 2319 Sorted by residual: chirality pdb=" P U A 64 " pdb=" OP1 U A 64 " pdb=" OP2 U A 64 " pdb=" O5' U A 64 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C2' C A 67 " pdb=" C3' C A 67 " pdb=" O2' C A 67 " pdb=" C1' C A 67 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' C A 91 " pdb=" C3' C A 91 " pdb=" O2' C A 91 " pdb=" C1' C A 91 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.090 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- 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= 0.285 Angle : 0.679 7.220 20341 Z= 0.423 Chirality : 0.066 0.310 2319 Planarity : 0.003 0.044 2088 Dihedral : 17.575 89.047 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 0.00411 / 0.29 (14623) covalent geometry : angle 0.67940 / 0.42 (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 : 0.484 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: 0.1326 time to fit residues: 39.6549 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 : 0.488 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.063312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.048271 restraints weight = 117062.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049704 restraints weight = 58773.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.050520 restraints weight = 38577.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051063 restraints weight = 29911.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.051421 restraints weight = 25574.651| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14623 Z= 0.204 Angle : 0.997 20.375 20341 Z= 0.432 Chirality : 0.092 1.632 2319 Planarity : 0.004 0.051 2088 Dihedral : 19.535 136.283 3131 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.16 % Allowed : 1.64 % 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: 0.83 (0.23), residues: 1353 helix: 1.35 (0.20), residues: 680 sheet: 0.01 (0.49), residues: 110 loop : -0.23 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 324 TYR 0.015 0.002 TYR B1013 PHE 0.025 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 0.00404 / 0.20 (14623) covalent geometry : angle 0.99736 / 0.43 (20341) hydrogen bonds : bond 0.05164 / 3.45 ( 640) hydrogen bonds : angle 4.69097 / 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 : 0.366 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: B 161 MET cc_start: 0.8983 (tpp) cc_final: 0.8756 (tpp) REVERT: B 534 MET cc_start: 0.3183 (mtp) cc_final: 0.1981 (ptp) REVERT: B 631 MET cc_start: 0.9417 (mmp) cc_final: 0.9187 (mmt) REVERT: B 659 TRP cc_start: 0.7736 (m100) cc_final: 0.7332 (m100) REVERT: B 727 LEU cc_start: 0.9121 (mt) cc_final: 0.8890 (mt) REVERT: B 781 MET cc_start: 0.8507 (mmm) cc_final: 0.8232 (mmm) REVERT: B 822 MET cc_start: 0.9564 (tpt) cc_final: 0.9224 (tpp) REVERT: B 935 LEU cc_start: 0.9486 (mm) cc_final: 0.9263 (mm) REVERT: B 966 PHE cc_start: 0.9259 (t80) cc_final: 0.8819 (t80) REVERT: B 1046 PHE cc_start: 0.7771 (m-10) cc_final: 0.7327 (m-80) REVERT: B 1213 MET cc_start: 0.7748 (mtm) cc_final: 0.7238 (ttm) REVERT: B 1219 GLU cc_start: 0.8903 (tt0) cc_final: 0.8375 (tm-30) REVERT: B 1350 GLN cc_start: 0.8757 (mt0) cc_final: 0.8474 (mm-40) outliers start: 2 outliers final: 0 residues processed: 120 average time/residue: 0.1194 time to fit residues: 21.3082 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 : 0.436 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 30.0000 chunk 118 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 40.0000 chunk 53 optimal weight: 0.1980 chunk 137 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN B 459 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.061325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.045914 restraints weight = 106542.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.047364 restraints weight = 55668.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.048281 restraints weight = 37086.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.048762 restraints weight = 28562.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.049113 restraints weight = 24707.394| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14623 Z= 0.136 Angle : 0.735 13.908 20341 Z= 0.339 Chirality : 0.063 0.889 2319 Planarity : 0.004 0.047 2088 Dihedral : 19.418 152.330 3131 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.16 % Allowed : 1.89 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.23), residues: 1353 helix: 1.52 (0.20), residues: 682 sheet: -0.05 (0.48), residues: 110 loop : -0.17 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 661 TYR 0.025 0.001 TYR B1336 PHE 0.018 0.001 PHE B1313 TRP 0.010 0.001 TRP B 18 HIS 0.004 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (14623) covalent geometry : angle 0.73456 / 0.34 (20341) hydrogen bonds : bond 0.03988 / 2.60 ( 640) hydrogen bonds : angle 4.41000 / 3.04 ( 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 110 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.492 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 139 ARG cc_start: 0.9331 (mtm180) cc_final: 0.8775 (ttm170) REVERT: B 321 MET cc_start: 0.9134 (tpp) cc_final: 0.8875 (tpp) REVERT: B 383 MET cc_start: 0.8651 (mmp) cc_final: 0.8137 (mmm) REVERT: B 459 ASN cc_start: 0.4553 (OUTLIER) cc_final: 0.4350 (t0) REVERT: B 534 MET cc_start: 0.2774 (mtp) cc_final: 0.1906 (ptp) REVERT: B 631 MET cc_start: 0.9434 (mmp) cc_final: 0.9204 (mmt) REVERT: B 659 TRP cc_start: 0.7831 (m100) cc_final: 0.7334 (m100) REVERT: B 718 ASP cc_start: 0.9270 (m-30) cc_final: 0.8750 (p0) REVERT: B 781 MET cc_start: 0.8782 (mmm) cc_final: 0.8469 (mmm) REVERT: B 822 MET cc_start: 0.9546 (tpt) cc_final: 0.9153 (tpp) REVERT: B 1213 MET cc_start: 0.7763 (mtm) cc_final: 0.7454 (ttm) REVERT: B 1350 GLN cc_start: 0.8903 (mt0) cc_final: 0.8630 (mm-40) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.1105 time to fit residues: 18.4086 Evaluate side-chains 73 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 3.9990 chunk 132 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.058325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043146 restraints weight = 110858.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.044473 restraints weight = 59388.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.045233 restraints weight = 40304.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.045754 restraints weight = 31841.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.046084 restraints weight = 27452.897| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14623 Z= 0.221 Angle : 0.748 13.100 20341 Z= 0.353 Chirality : 0.055 0.556 2319 Planarity : 0.004 0.048 2088 Dihedral : 19.413 147.735 3131 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 1.66 (0.20), residues: 673 sheet: 0.14 (0.58), residues: 82 loop : -0.16 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 78 TYR 0.023 0.002 TYR B 136 PHE 0.020 0.002 PHE B1008 TRP 0.016 0.002 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (14623) covalent geometry : angle 0.74772 / 0.35 (20341) hydrogen bonds : bond 0.05712 / 3.83 ( 640) hydrogen bonds : angle 4.61754 / 3.19 ( 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 95 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.359 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 139 ARG cc_start: 0.9328 (mtm180) cc_final: 0.8326 (mtm180) REVERT: B 161 MET cc_start: 0.9081 (tpp) cc_final: 0.8528 (tpp) REVERT: B 321 MET cc_start: 0.9080 (tpp) cc_final: 0.8863 (tpt) REVERT: B 383 MET cc_start: 0.8670 (mmp) cc_final: 0.8150 (mmm) REVERT: B 534 MET cc_start: 0.3505 (mtp) cc_final: 0.2705 (ptp) REVERT: B 631 MET cc_start: 0.9458 (mmp) cc_final: 0.9252 (mmt) REVERT: B 659 TRP cc_start: 0.7965 (m100) cc_final: 0.7481 (m100) REVERT: B 718 ASP cc_start: 0.9275 (m-30) cc_final: 0.8766 (p0) REVERT: B 740 THR cc_start: 0.8926 (m) cc_final: 0.8694 (m) REVERT: B 780 ARG cc_start: 0.9136 (mtt180) cc_final: 0.8664 (mtm-85) REVERT: B 781 MET cc_start: 0.8986 (mmm) cc_final: 0.8363 (mmm) REVERT: B 822 MET cc_start: 0.9599 (tpt) cc_final: 0.9280 (tpp) REVERT: B 966 PHE cc_start: 0.9171 (t80) cc_final: 0.8826 (t80) REVERT: B 1213 MET cc_start: 0.8019 (mtm) cc_final: 0.7471 (ttm) REVERT: B 1219 GLU cc_start: 0.9012 (tt0) cc_final: 0.8580 (tt0) REVERT: B 1242 TYR cc_start: 0.7546 (t80) cc_final: 0.7213 (t80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1170 time to fit residues: 16.9274 Evaluate side-chains 70 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 9.9990 chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 175 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 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 = 0.3618 r_free = 0.3618 target = 0.057247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.042408 restraints weight = 111807.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.043672 restraints weight = 60183.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.044460 restraints weight = 40865.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.044968 restraints weight = 32047.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.045227 restraints weight = 27622.475| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14623 Z= 0.235 Angle : 0.729 12.103 20341 Z= 0.352 Chirality : 0.052 0.445 2319 Planarity : 0.005 0.066 2088 Dihedral : 19.538 143.242 3131 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 0.89 (0.23), residues: 1353 helix: 1.52 (0.20), residues: 675 sheet: -0.10 (0.59), residues: 77 loop : -0.32 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 586 TYR 0.022 0.002 TYR B 373 PHE 0.018 0.002 PHE B 32 TRP 0.025 0.002 TRP B 464 HIS 0.015 0.002 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.24 (14623) covalent geometry : angle 0.72915 / 0.35 (20341) hydrogen bonds : bond 0.05194 / 3.46 ( 640) hydrogen bonds : angle 4.72014 / 3.27 ( 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 91 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.444 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: B 161 MET cc_start: 0.9008 (tpp) cc_final: 0.8729 (tpp) REVERT: B 383 MET cc_start: 0.8655 (mmp) cc_final: 0.8149 (mmm) REVERT: B 534 MET cc_start: 0.3535 (mtp) cc_final: 0.2832 (ptp) REVERT: B 631 MET cc_start: 0.9429 (mmp) cc_final: 0.9224 (mmt) REVERT: B 718 ASP cc_start: 0.9259 (m-30) cc_final: 0.8780 (p0) REVERT: B 780 ARG cc_start: 0.9145 (mtt180) cc_final: 0.8612 (mtm-85) REVERT: B 781 MET cc_start: 0.9109 (mmm) cc_final: 0.8409 (mmm) REVERT: B 822 MET cc_start: 0.9561 (tpt) cc_final: 0.8624 (tpp) REVERT: B 1169 MET cc_start: 0.9017 (mmt) cc_final: 0.8808 (mmt) REVERT: B 1213 MET cc_start: 0.7977 (mtm) cc_final: 0.7328 (ttm) REVERT: B 1219 GLU cc_start: 0.8955 (tt0) cc_final: 0.8536 (tt0) REVERT: B 1242 TYR cc_start: 0.7617 (t80) cc_final: 0.7273 (t80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1075 time to fit residues: 15.1768 Evaluate side-chains 68 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 0.7980 chunk 102 optimal weight: 40.0000 chunk 47 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 95 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN B 899 ASN ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.057683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042705 restraints weight = 110876.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.043947 restraints weight = 59810.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.044787 restraints weight = 40908.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.045234 restraints weight = 32040.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.045558 restraints weight = 27758.309| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14623 Z= 0.163 Angle : 0.659 11.154 20341 Z= 0.317 Chirality : 0.049 0.410 2319 Planarity : 0.004 0.046 2088 Dihedral : 19.390 135.906 3131 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.08 % Allowed : 0.99 % 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: 1.05 (0.23), residues: 1353 helix: 1.67 (0.20), residues: 678 sheet: -0.28 (0.55), residues: 87 loop : -0.25 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 832 TYR 0.031 0.002 TYR B 823 PHE 0.017 0.001 PHE B 970 TRP 0.018 0.002 TRP B 464 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (14623) covalent geometry : angle 0.65851 / 0.32 (20341) hydrogen bonds : bond 0.04404 / 2.90 ( 640) hydrogen bonds : angle 4.53152 / 3.13 ( 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 96 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.485 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: B 383 MET cc_start: 0.8675 (mmp) cc_final: 0.8150 (mmm) REVERT: B 534 MET cc_start: 0.3957 (mtp) cc_final: 0.3227 (ptp) REVERT: B 718 ASP cc_start: 0.9299 (m-30) cc_final: 0.8806 (p0) REVERT: B 780 ARG cc_start: 0.9109 (mtt180) cc_final: 0.8587 (mtm-85) REVERT: B 781 MET cc_start: 0.9143 (mmm) cc_final: 0.8492 (mmm) REVERT: B 822 MET cc_start: 0.9450 (tpt) cc_final: 0.9049 (tpp) REVERT: B 1198 LEU cc_start: 0.8720 (mp) cc_final: 0.8502 (mp) REVERT: B 1213 MET cc_start: 0.7978 (mtm) cc_final: 0.7306 (ttm) REVERT: B 1219 GLU cc_start: 0.8934 (tt0) cc_final: 0.8509 (tt0) REVERT: B 1242 TYR cc_start: 0.7698 (t80) cc_final: 0.7340 (t80) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.0978 time to fit residues: 14.7745 Evaluate side-chains 69 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 3.9990 chunk 111 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 118 optimal weight: 0.0070 chunk 123 optimal weight: 20.0000 chunk 145 optimal weight: 50.0000 chunk 26 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 overall best weight: 4.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 46 ASN B 77 ASN B 511 HIS ** 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** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.056954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041943 restraints weight = 111674.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.043281 restraints weight = 58731.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.044046 restraints weight = 39362.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.044563 restraints weight = 30886.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.044899 restraints weight = 26579.447| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14623 Z= 0.194 Angle : 0.673 10.898 20341 Z= 0.325 Chirality : 0.048 0.399 2319 Planarity : 0.004 0.047 2088 Dihedral : 19.393 135.945 3131 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 1.05 (0.23), residues: 1353 helix: 1.71 (0.20), residues: 676 sheet: -0.28 (0.55), residues: 87 loop : -0.29 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.014 0.002 TYR B 450 PHE 0.019 0.002 PHE B 970 TRP 0.026 0.003 TRP B 659 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (14623) covalent geometry : angle 0.67263 / 0.32 (20341) hydrogen bonds : bond 0.04816 / 3.19 ( 640) hydrogen bonds : angle 4.56204 / 3.16 ( 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 89 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.466 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: B 139 ARG cc_start: 0.9429 (mtm180) cc_final: 0.9018 (mmm-85) REVERT: B 383 MET cc_start: 0.8678 (mmp) cc_final: 0.8148 (mmm) REVERT: B 534 MET cc_start: 0.3793 (mtp) cc_final: 0.3154 (ptp) REVERT: B 631 MET cc_start: 0.9341 (mmt) cc_final: 0.9058 (mmm) REVERT: B 718 ASP cc_start: 0.9301 (m-30) cc_final: 0.8801 (p0) REVERT: B 780 ARG cc_start: 0.9078 (mtt180) cc_final: 0.8551 (mtm-85) REVERT: B 781 MET cc_start: 0.9233 (mmm) cc_final: 0.8564 (mmm) REVERT: B 794 GLN cc_start: 0.9581 (mp-120) cc_final: 0.9354 (mm-40) REVERT: B 822 MET cc_start: 0.9523 (tpt) cc_final: 0.9200 (tpp) REVERT: B 1198 LEU cc_start: 0.8746 (mp) cc_final: 0.8537 (mp) REVERT: B 1213 MET cc_start: 0.7953 (mtm) cc_final: 0.7263 (ttm) REVERT: B 1219 GLU cc_start: 0.8942 (tt0) cc_final: 0.8535 (tt0) REVERT: B 1242 TYR cc_start: 0.7770 (t80) cc_final: 0.7406 (t80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1045 time to fit residues: 14.4984 Evaluate side-chains 70 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 5.9990 chunk 145 optimal weight: 50.0000 chunk 117 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 54 optimal weight: 50.0000 chunk 125 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** 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** ** 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 = 0.056053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.040586 restraints weight = 120059.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.041870 restraints weight = 66357.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.042613 restraints weight = 45686.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.043097 restraints weight = 36396.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.043409 restraints weight = 31698.520| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14623 Z= 0.225 Angle : 0.713 12.390 20341 Z= 0.344 Chirality : 0.048 0.414 2319 Planarity : 0.004 0.047 2088 Dihedral : 19.300 135.783 3131 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 0.94 (0.23), residues: 1353 helix: 1.60 (0.20), residues: 675 sheet: -0.45 (0.56), residues: 84 loop : -0.30 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.035 0.002 TYR B 5 PHE 0.020 0.002 PHE B1105 TRP 0.023 0.003 TRP B 464 HIS 0.009 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 (14623) covalent geometry : angle 0.71347 / 0.34 (20341) hydrogen bonds : bond 0.05288 / 3.53 ( 640) hydrogen bonds : angle 4.70687 / 3.27 ( 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 81 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 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: 0.8140 (mmm) REVERT: B 534 MET cc_start: 0.4148 (mtp) cc_final: 0.3494 (ptp) REVERT: B 631 MET cc_start: 0.9343 (mmt) cc_final: 0.9117 (mmm) REVERT: B 718 ASP cc_start: 0.9355 (m-30) cc_final: 0.8868 (p0) REVERT: B 780 ARG cc_start: 0.8981 (mtt180) cc_final: 0.8464 (mtm-85) REVERT: B 781 MET cc_start: 0.9222 (mmm) cc_final: 0.8526 (mmm) REVERT: B 1043 MET cc_start: 0.9442 (tpt) cc_final: 0.9231 (tpt) REVERT: B 1198 LEU cc_start: 0.8744 (mp) cc_final: 0.8529 (mp) REVERT: B 1213 MET cc_start: 0.7936 (mtm) cc_final: 0.7221 (ttm) REVERT: B 1242 TYR cc_start: 0.7995 (t80) cc_final: 0.7614 (t80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1043 time to fit residues: 13.0798 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 : 0.498 ------------------------------------------------------------------------------- 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: 7.9990 chunk 21 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 85 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 68 optimal weight: 50.0000 chunk 107 optimal weight: 0.0470 chunk 32 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 overall best weight: 6.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** 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** B 863 ASN ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.055319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040037 restraints weight = 122192.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.041273 restraints weight = 67388.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.041966 restraints weight = 46631.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.042444 restraints weight = 37546.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042745 restraints weight = 32665.018| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14623 Z= 0.259 Angle : 0.745 11.389 20341 Z= 0.362 Chirality : 0.048 0.433 2319 Planarity : 0.005 0.093 2088 Dihedral : 19.317 136.281 3131 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: 0.77 (0.23), residues: 1353 helix: 1.44 (0.20), residues: 674 sheet: -0.69 (0.54), residues: 84 loop : -0.32 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 139 TYR 0.038 0.002 TYR B 5 PHE 0.017 0.002 PHE B1204 TRP 0.026 0.003 TRP B 464 HIS 0.010 0.002 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.26 (14623) covalent geometry : angle 0.74499 / 0.36 (20341) hydrogen bonds : bond 0.05774 / 3.88 ( 640) hydrogen bonds : angle 4.87307 / 3.39 ( 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 78 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.345 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: B 383 MET cc_start: 0.8699 (mmp) cc_final: 0.8108 (mmm) REVERT: B 534 MET cc_start: 0.4006 (mtp) cc_final: 0.3428 (ptp) REVERT: B 631 MET cc_start: 0.9332 (mmt) cc_final: 0.9070 (mmm) REVERT: B 718 ASP cc_start: 0.9365 (m-30) cc_final: 0.8856 (p0) REVERT: B 780 ARG cc_start: 0.8994 (mtt180) cc_final: 0.8483 (mtm-85) REVERT: B 781 MET cc_start: 0.9238 (mmm) cc_final: 0.8622 (mmm) REVERT: B 822 MET cc_start: 0.9364 (mmp) cc_final: 0.8707 (mmm) REVERT: B 1198 LEU cc_start: 0.8813 (mp) cc_final: 0.8603 (mp) REVERT: B 1219 GLU cc_start: 0.8937 (tt0) cc_final: 0.8522 (tt0) REVERT: B 1242 TYR cc_start: 0.8013 (t80) cc_final: 0.7645 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0983 time to fit residues: 12.3056 Evaluate side-chains 61 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 8.9990 chunk 119 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN ** B1044 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 = 0.3575 r_free = 0.3575 target = 0.056030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040647 restraints weight = 120137.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.041924 restraints weight = 65791.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042628 restraints weight = 45229.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.043112 restraints weight = 36380.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.043406 restraints weight = 31812.910| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14623 Z= 0.180 Angle : 0.668 10.695 20341 Z= 0.324 Chirality : 0.047 0.424 2319 Planarity : 0.004 0.047 2088 Dihedral : 19.188 136.620 3131 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 0.94 (0.23), residues: 1353 helix: 1.61 (0.20), residues: 675 sheet: -0.70 (0.56), residues: 79 loop : -0.27 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.022 0.002 TYR B1265 PHE 0.017 0.002 PHE B1105 TRP 0.019 0.002 TRP B 464 HIS 0.007 0.001 HIS B 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (14623) covalent geometry : angle 0.66781 / 0.32 (20341) hydrogen bonds : bond 0.04606 / 3.07 ( 640) hydrogen bonds : angle 4.69536 / 3.26 ( 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 80 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.414 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: B 161 MET cc_start: 0.9117 (tpp) cc_final: 0.8787 (tpp) REVERT: B 174 LEU cc_start: 0.9190 (pp) cc_final: 0.8735 (mp) REVERT: B 383 MET cc_start: 0.8685 (mmp) cc_final: 0.8053 (mmm) REVERT: B 534 MET cc_start: 0.3725 (mtp) cc_final: 0.3202 (ptp) REVERT: B 631 MET cc_start: 0.9341 (mmt) cc_final: 0.9086 (mmm) REVERT: B 718 ASP cc_start: 0.9362 (m-30) cc_final: 0.8847 (p0) REVERT: B 722 GLU cc_start: 0.9487 (mp0) cc_final: 0.9024 (mp0) REVERT: B 780 ARG cc_start: 0.8977 (mtt180) cc_final: 0.8452 (mtm-85) REVERT: B 781 MET cc_start: 0.9243 (mmm) cc_final: 0.8542 (mmm) REVERT: B 822 MET cc_start: 0.9128 (mmp) cc_final: 0.8554 (mmm) REVERT: B 923 GLU cc_start: 0.6822 (tp30) cc_final: 0.6519 (mp0) REVERT: B 1043 MET cc_start: 0.9352 (tpt) cc_final: 0.9006 (tpt) REVERT: B 1169 MET cc_start: 0.8437 (mmp) cc_final: 0.7388 (mtp) REVERT: B 1198 LEU cc_start: 0.8771 (mp) cc_final: 0.8551 (mp) REVERT: B 1219 GLU cc_start: 0.8883 (tt0) cc_final: 0.8484 (tt0) REVERT: B 1242 TYR cc_start: 0.7957 (t80) cc_final: 0.7586 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1037 time to fit residues: 13.7059 Evaluate side-chains 63 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 8.9990 chunk 133 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN B 863 ASN ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.055931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040623 restraints weight = 119958.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041863 restraints weight = 66620.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042576 restraints weight = 46207.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.043071 restraints weight = 37084.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.043365 restraints weight = 32322.999| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14623 Z= 0.184 Angle : 0.661 10.435 20341 Z= 0.323 Chirality : 0.047 0.419 2319 Planarity : 0.004 0.046 2088 Dihedral : 19.118 136.314 3131 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.97 (0.23), residues: 1353 helix: 1.62 (0.20), residues: 678 sheet: -0.54 (0.58), residues: 79 loop : -0.27 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.030 0.002 TYR B 5 PHE 0.015 0.002 PHE B1181 TRP 0.019 0.002 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (14623) covalent geometry : angle 0.66091 / 0.32 (20341) hydrogen bonds : bond 0.04790 / 3.20 ( 640) hydrogen bonds : angle 4.67226 / 3.25 ( 1727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.43 seconds wall clock time: 44 minutes 17.47 seconds (2657.47 seconds total)