Starting phenix.real_space_refine on Sat Sep 12 18:18:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4c_14493/09_2026/7z4c_14493.cif" } resolution = 3.87 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= 0.002 sd= 0.021 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 3714 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 145 5.49 5 S 23 5.16 5 C 8486 2.51 5 N 2483 2.21 5 O 3043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.22s 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: 14180 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 589 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1910 Classifications: {'DNA': 1, 'RNAv2': 89} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 76} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 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 Time building chain proxies: 3.17, per 1000 atoms: 0.22 Number of scatterers: 14180 At special positions: 0 Unit cell: (92.3, 124.15, 124.8, 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 145 15.00 O 3043 8.00 N 2483 7.00 C 8486 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: 1.10 Conformation dependent library (CDL) restraints added in 465.3 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: 67 helices and 10 sheets defined 54.4% alpha, 8.1% beta 51 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.763A 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 removed outlier: 3.759A pdb=" N ASP B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.905A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.715A pdb=" N SER B 320 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.522A 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 404 through 410 removed outlier: 3.900A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.351A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.603A pdb=" N LYS B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 removed outlier: 3.779A pdb=" N VAL B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.899A pdb=" N THR B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 525 removed outlier: 3.554A pdb=" N GLU B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.657A 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 625 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 643 removed outlier: 4.529A pdb=" N HIS B 641 " --> pdb=" O THR B 638 " (cutoff:3.500A) 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: 4.276A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 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 804 through 807 removed outlier: 3.705A pdb=" N GLN B 807 " --> pdb=" O THR B 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 804 through 807' Processing helix chain 'B' and resid 808 through 817 removed outlier: 3.642A pdb=" N TYR B 812 " --> pdb=" O ASN B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.538A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 3.555A pdb=" N VAL B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.709A 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 901 through 906 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: 4.206A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 970 " --> pdb=" O PHE B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.530A 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 1043 through 1047 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 removed outlier: 3.513A pdb=" N TYR B1131 " --> pdb=" O ASP B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.582A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1278 removed outlier: 3.616A pdb=" N SER B1274 " --> pdb=" O ILE B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1306 through 1311 removed outlier: 3.976A pdb=" N HIS B1311 " --> pdb=" O GLU B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.592A pdb=" N LEU B1315 " --> pdb=" O LEU B1312 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B1317 " --> pdb=" O THR B1314 " (cutoff:3.500A) Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 removed outlier: 4.152A pdb=" N ASN B 758 " --> pdb=" O TYR B 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.821A pdb=" N LEU B 35 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B1359 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.759A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 3.911A 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 removed outlier: 3.874A pdb=" N ASP B 837 " --> pdb=" O THR B 858 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR B 858 " --> pdb=" O ASP B 837 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1051 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 1106 through 1111 removed outlier: 6.866A pdb=" N LYS B1107 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B1133 " --> pdb=" O LEU B1111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.730A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 512 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 125 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3110 1.33 - 1.45: 3728 1.45 - 1.57: 7575 1.57 - 1.69: 290 1.69 - 1.81: 44 Bond restraints: 14747 Sorted by residual: bond pdb=" C1' DC C 5 " pdb=" N1 DC C 5 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" C3' DC C 2 " pdb=" C2' DC C 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.51e+00 bond pdb=" C1' DT D -6 " pdb=" N1 DT D -6 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.60e+00 bond pdb=" C3' DG C -6 " pdb=" C2' DG C -6 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.41e+00 ... (remaining 14742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 19522 1.21 - 2.41: 684 2.41 - 3.62: 279 3.62 - 4.82: 37 4.82 - 6.03: 11 Bond angle restraints: 20533 Sorted by residual: angle pdb=" N3 DT C 7 " pdb=" C4 DT C 7 " pdb=" O4 DT C 7 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.30e+01 angle pdb=" O PHE B 446 " pdb=" C PHE B 446 " pdb=" N ARG B 447 " ideal model delta sigma weight residual 122.96 128.75 -5.79 1.26e+00 6.30e-01 2.11e+01 angle pdb=" N3 DT D -15 " pdb=" C4 DT D -15 " pdb=" O4 DT D -15 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT C 14 " pdb=" C4 DT C 14 " pdb=" O4 DT C 14 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT D -17 " pdb=" C4 DT D -17 " pdb=" O4 DT D -17 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 20528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 8199 35.93 - 71.86: 440 71.86 - 107.78: 9 107.78 - 143.71: 1 143.71 - 179.64: 2 Dihedral angle restraints: 8651 sinusoidal: 4661 harmonic: 3990 Sorted by residual: dihedral pdb=" C4' A A 88 " pdb=" C3' A A 88 " pdb=" C2' A A 88 " pdb=" C1' A A 88 " ideal model delta sinusoidal sigma weight residual 36.35 -37.11 73.46 1 3.10e+00 1.04e-01 7.15e+02 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 36.34 -36.95 73.30 1 3.10e+00 1.04e-01 7.12e+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 -36.81 73.16 1 3.10e+00 1.04e-01 7.10e+02 ... (remaining 8648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1930 0.056 - 0.113: 277 0.113 - 0.169: 19 0.169 - 0.225: 36 0.225 - 0.282: 80 Chirality restraints: 2342 Sorted by residual: chirality pdb=" C2' G A 43 " pdb=" C3' G A 43 " pdb=" O2' G A 43 " pdb=" C1' G A 43 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' U A 59 " pdb=" C3' U A 59 " pdb=" O2' U A 59 " pdb=" C1' U A 59 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" P G A 81 " pdb=" OP1 G A 81 " pdb=" OP2 G A 81 " pdb=" O5' G A 81 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2339 not shown) Planarity restraints: 2093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 13 " -0.025 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" N1 U A 13 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U A 13 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U A 13 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 13 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U A 13 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U A 13 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U A 13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U A 13 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 454 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C PRO B 454 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 454 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 455 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 12 " -0.023 2.00e-02 2.50e+03 1.05e-02 3.06e+00 pdb=" N9 A A 12 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A A 12 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 12 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A 12 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 12 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 2090 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2437 2.77 - 3.30: 13375 3.30 - 3.83: 24711 3.83 - 4.37: 28632 4.37 - 4.90: 45023 Nonbonded interactions: 114178 Sorted by model distance: nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.232 3.040 nonbonded pdb=" O LEU B 551 " pdb=" OG1 THR B 555 " model vdw 2.235 3.040 nonbonded pdb=" O HIS B 799 " pdb=" OH TYR B 815 " model vdw 2.245 3.040 nonbonded pdb=" O2' U A 56 " pdb=" N2 G A 58 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLU B1357 " pdb=" NH1 ARG B1359 " model vdw 2.265 3.120 ... (remaining 114173 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: 4.750 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.040 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.003 0.047 14747 Z= 0.242 Angle : 0.606 6.029 20533 Z= 0.378 Chirality : 0.064 0.282 2342 Planarity : 0.003 0.031 2093 Dihedral : 17.029 179.639 6071 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.06 % Allowed : 4.28 % Favored : 93.67 % 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: 1.93 (0.21), residues: 656 sheet: -0.18 (0.48), residues: 118 loop : -0.52 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.011 0.001 TYR B 155 PHE 0.009 0.001 PHE B1276 TRP 0.009 0.001 TRP B 464 HIS 0.003 0.001 HIS B1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.24 (14747) covalent geometry : angle 0.60585 / 0.38 (20533) hydrogen bonds : bond 0.15410 / 17.90 ( 637) hydrogen bonds : angle 5.43938 / 7.41 ( 1709) *********************** 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 160 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.506 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 174 LEU cc_start: 0.9221 (pp) cc_final: 0.8865 (tp) REVERT: B 534 MET cc_start: 0.6025 (mtp) cc_final: 0.5743 (ptp) REVERT: B 703 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 727 LEU cc_start: 0.8780 (mt) cc_final: 0.8235 (mt) REVERT: B 734 LYS cc_start: 0.9386 (mtmt) cc_final: 0.9087 (mtmt) REVERT: B 782 LYS cc_start: 0.9800 (ttmt) cc_final: 0.9568 (ptmm) REVERT: B 815 TYR cc_start: 0.9516 (m-80) cc_final: 0.8945 (m-80) REVERT: B 1004 LEU cc_start: 0.8927 (mt) cc_final: 0.8512 (mt) REVERT: B 1099 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 1333 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8684 (ptt180) outliers start: 25 outliers final: 6 residues processed: 156 average time/residue: 0.1380 time to fit residues: 30.7775 Evaluate side-chains 83 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 HIS B 415 HIS B 459 ASN B 612 ASN B 698 HIS ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN B 885 GLN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN B1305 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.050611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.036050 restraints weight = 107793.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.037392 restraints weight = 53166.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038109 restraints weight = 34816.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.038637 restraints weight = 27463.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.038889 restraints weight = 23698.163| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14747 Z= 0.257 Angle : 0.995 22.768 20533 Z= 0.438 Chirality : 0.084 1.138 2342 Planarity : 0.004 0.030 2093 Dihedral : 19.507 175.553 3202 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.06 % Allowed : 9.46 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1353 helix: 2.01 (0.21), residues: 659 sheet: 0.06 (0.54), residues: 87 loop : -0.60 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 832 TYR 0.024 0.002 TYR B 823 PHE 0.011 0.001 PHE B 518 TRP 0.009 0.001 TRP B 18 HIS 0.006 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.26 (14747) covalent geometry : angle 0.99527 / 0.44 (20533) hydrogen bonds : bond 0.05487 / 6.09 ( 637) hydrogen bonds : angle 4.69590 / 6.27 ( 1709) *********************** 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 97 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 LEU cc_start: 0.9201 (pp) cc_final: 0.8729 (tp) REVERT: B 383 MET cc_start: 0.8486 (mmp) cc_final: 0.8262 (mmt) REVERT: B 534 MET cc_start: 0.6340 (mtp) cc_final: 0.5885 (ptp) REVERT: B 703 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8998 (p) REVERT: B 727 LEU cc_start: 0.8615 (mt) cc_final: 0.8211 (mt) REVERT: B 815 TYR cc_start: 0.9548 (m-80) cc_final: 0.8998 (m-80) REVERT: B 1099 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 1169 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8403 (mmm) REVERT: B 1213 MET cc_start: 0.6121 (mtp) cc_final: 0.5904 (mtp) REVERT: B 1333 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8383 (ptt180) outliers start: 25 outliers final: 14 residues processed: 91 average time/residue: 0.1279 time to fit residues: 17.4598 Evaluate side-chains 78 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.0010 chunk 63 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 826 GLN B 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.050786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036308 restraints weight = 107760.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.037630 restraints weight = 52443.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.038357 restraints weight = 34364.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.038860 restraints weight = 27148.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039125 restraints weight = 23561.626| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14747 Z= 0.153 Angle : 0.731 16.837 20533 Z= 0.335 Chirality : 0.061 0.839 2342 Planarity : 0.003 0.031 2093 Dihedral : 19.544 174.667 3202 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.73 % Allowed : 10.94 % Favored : 87.34 % 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: 1.15 (0.23), residues: 1353 helix: 2.04 (0.21), residues: 658 sheet: 0.12 (0.49), residues: 119 loop : -0.61 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 778 TYR 0.013 0.001 TYR B 823 PHE 0.014 0.001 PHE B 446 TRP 0.014 0.001 TRP B 18 HIS 0.005 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (14747) covalent geometry : angle 0.73117 / 0.33 (20533) hydrogen bonds : bond 0.04355 / 4.76 ( 637) hydrogen bonds : angle 4.32492 / 5.77 ( 1709) *********************** 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 89 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.411 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 103 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8545 (pp20) REVERT: B 174 LEU cc_start: 0.9164 (pp) cc_final: 0.8655 (tp) REVERT: B 534 MET cc_start: 0.6506 (mtp) cc_final: 0.6050 (ptp) REVERT: B 703 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8993 (p) REVERT: B 727 LEU cc_start: 0.8630 (mt) cc_final: 0.8055 (mt) REVERT: B 751 MET cc_start: 0.9089 (tpp) cc_final: 0.8716 (ttm) REVERT: B 815 TYR cc_start: 0.9515 (m-80) cc_final: 0.8982 (m-80) REVERT: B 1021 MET cc_start: 0.8718 (mpp) cc_final: 0.8298 (mmp) REVERT: B 1043 MET cc_start: 0.8702 (tmm) cc_final: 0.8490 (tmm) REVERT: B 1093 ASN cc_start: 0.8496 (m-40) cc_final: 0.7876 (m-40) REVERT: B 1099 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 1333 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8158 (ptt180) outliers start: 21 outliers final: 12 residues processed: 84 average time/residue: 0.1251 time to fit residues: 15.6491 Evaluate side-chains 79 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 990 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 = 0.3337 r_free = 0.3337 target = 0.048976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.034622 restraints weight = 111301.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.035870 restraints weight = 54771.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036589 restraints weight = 36023.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.037102 restraints weight = 28452.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.037304 restraints weight = 24604.391| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14747 Z= 0.237 Angle : 0.745 13.994 20533 Z= 0.350 Chirality : 0.055 0.597 2342 Planarity : 0.004 0.053 2093 Dihedral : 19.583 174.327 3202 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.55 % Allowed : 10.86 % Favored : 86.60 % 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: 1.89 (0.21), residues: 667 sheet: 0.50 (0.55), residues: 93 loop : -0.73 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 864 TYR 0.014 0.001 TYR B 988 PHE 0.015 0.002 PHE B 446 TRP 0.009 0.002 TRP B 659 HIS 0.007 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.24 (14747) covalent geometry : angle 0.74487 / 0.35 (20533) hydrogen bonds : bond 0.05157 / 5.63 ( 637) hydrogen bonds : angle 4.47221 / 5.95 ( 1709) *********************** 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 92 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.437 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 90 MET cc_start: 0.9503 (mmm) cc_final: 0.9273 (mmm) REVERT: B 703 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.9005 (p) REVERT: B 727 LEU cc_start: 0.8591 (mt) cc_final: 0.8120 (mt) REVERT: B 813 LEU cc_start: 0.9830 (mt) cc_final: 0.9584 (tp) REVERT: B 815 TYR cc_start: 0.9541 (m-80) cc_final: 0.9029 (m-80) REVERT: B 822 MET cc_start: 0.9031 (mmp) cc_final: 0.8824 (mmp) REVERT: B 1021 MET cc_start: 0.8749 (mpp) cc_final: 0.8279 (tpp) REVERT: B 1043 MET cc_start: 0.8784 (tmm) cc_final: 0.8557 (tmm) REVERT: B 1093 ASN cc_start: 0.8578 (m-40) cc_final: 0.7903 (m-40) REVERT: B 1099 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8228 (mt-10) REVERT: B 1333 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8343 (ptt180) REVERT: B 1350 GLN cc_start: 0.8921 (mt0) cc_final: 0.8649 (tt0) outliers start: 31 outliers final: 19 residues processed: 86 average time/residue: 0.1103 time to fit residues: 14.3811 Evaluate side-chains 76 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.049388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.035048 restraints weight = 109505.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036345 restraints weight = 53358.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.037102 restraints weight = 34889.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.037583 restraints weight = 27330.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037825 restraints weight = 23679.389| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14747 Z= 0.159 Angle : 0.679 13.299 20533 Z= 0.319 Chirality : 0.052 0.570 2342 Planarity : 0.003 0.049 2093 Dihedral : 19.457 174.010 3200 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.38 % Allowed : 12.42 % Favored : 85.20 % 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: 1.92 (0.21), residues: 663 sheet: 0.50 (0.54), residues: 93 loop : -0.68 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 864 TYR 0.037 0.001 TYR B 823 PHE 0.012 0.001 PHE B 446 TRP 0.008 0.001 TRP B 18 HIS 0.007 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (14747) covalent geometry : angle 0.67948 / 0.32 (20533) hydrogen bonds : bond 0.04167 / 4.52 ( 637) hydrogen bonds : angle 4.30312 / 5.72 ( 1709) *********************** 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 89 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.520 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 90 MET cc_start: 0.9511 (mmm) cc_final: 0.9270 (mmm) REVERT: B 161 MET cc_start: 0.8928 (mpp) cc_final: 0.8661 (mpp) REVERT: B 383 MET cc_start: 0.8552 (mmp) cc_final: 0.8123 (mmt) REVERT: B 534 MET cc_start: 0.6084 (ttm) cc_final: 0.4686 (ptm) REVERT: B 667 ILE cc_start: 0.9746 (OUTLIER) cc_final: 0.9545 (mm) REVERT: B 703 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9003 (p) REVERT: B 727 LEU cc_start: 0.8625 (mt) cc_final: 0.7945 (mt) REVERT: B 801 VAL cc_start: 0.5228 (OUTLIER) cc_final: 0.4501 (p) REVERT: B 815 TYR cc_start: 0.9537 (m-80) cc_final: 0.9049 (m-80) REVERT: B 1021 MET cc_start: 0.8738 (mpp) cc_final: 0.8312 (mmp) REVERT: B 1043 MET cc_start: 0.8742 (tmm) cc_final: 0.8527 (tmm) REVERT: B 1093 ASN cc_start: 0.8537 (m-40) cc_final: 0.7872 (m-40) REVERT: B 1099 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8160 (mt-10) REVERT: B 1333 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8343 (ptt180) REVERT: B 1350 GLN cc_start: 0.8903 (mt0) cc_final: 0.8640 (tt0) outliers start: 29 outliers final: 18 residues processed: 83 average time/residue: 0.1281 time to fit residues: 16.0688 Evaluate side-chains 78 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 0.0470 chunk 133 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 91 optimal weight: 0.2980 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 990 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 = 0.3351 r_free = 0.3351 target = 0.049331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.035012 restraints weight = 108726.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036289 restraints weight = 53092.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037073 restraints weight = 34829.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.037465 restraints weight = 27102.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037781 restraints weight = 23844.009| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14747 Z= 0.154 Angle : 0.663 12.133 20533 Z= 0.313 Chirality : 0.049 0.518 2342 Planarity : 0.003 0.048 2093 Dihedral : 19.411 173.851 3200 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.22 % Allowed : 12.99 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1353 helix: 1.91 (0.21), residues: 668 sheet: 0.47 (0.53), residues: 93 loop : -0.64 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 820 TYR 0.015 0.001 TYR B1356 PHE 0.010 0.001 PHE B 446 TRP 0.009 0.001 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (14747) covalent geometry : angle 0.66254 / 0.31 (20533) hydrogen bonds : bond 0.04023 / 4.36 ( 637) hydrogen bonds : angle 4.18963 / 5.61 ( 1709) *********************** 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 88 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 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: B 90 MET cc_start: 0.9531 (mmm) cc_final: 0.9283 (mmm) REVERT: B 383 MET cc_start: 0.8552 (mmp) cc_final: 0.7966 (mmp) REVERT: B 534 MET cc_start: 0.6108 (ttm) cc_final: 0.4798 (ptm) REVERT: B 703 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 727 LEU cc_start: 0.8598 (mt) cc_final: 0.7922 (mt) REVERT: B 751 MET cc_start: 0.9057 (tpp) cc_final: 0.8582 (ttm) REVERT: B 778 ARG cc_start: 0.9402 (ptt180) cc_final: 0.9138 (ptp90) REVERT: B 801 VAL cc_start: 0.5158 (OUTLIER) cc_final: 0.4473 (p) REVERT: B 813 LEU cc_start: 0.9828 (mt) cc_final: 0.9584 (tp) REVERT: B 815 TYR cc_start: 0.9520 (m-80) cc_final: 0.9051 (m-80) REVERT: B 1021 MET cc_start: 0.8771 (mpp) cc_final: 0.8309 (mmp) REVERT: B 1043 MET cc_start: 0.8742 (tmm) cc_final: 0.8526 (tmm) REVERT: B 1099 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 1219 GLU cc_start: 0.8046 (tt0) cc_final: 0.7768 (mt-10) REVERT: B 1333 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8334 (ptt180) REVERT: B 1350 GLN cc_start: 0.8901 (mt0) cc_final: 0.8582 (tt0) outliers start: 27 outliers final: 17 residues processed: 84 average time/residue: 0.1273 time to fit residues: 16.1574 Evaluate side-chains 74 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 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 = 0.3319 r_free = 0.3319 target = 0.048114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.033895 restraints weight = 112361.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.035125 restraints weight = 55197.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.035832 restraints weight = 36304.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.036310 restraints weight = 28680.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.036511 restraints weight = 24867.158| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14747 Z= 0.249 Angle : 0.737 12.798 20533 Z= 0.349 Chirality : 0.050 0.524 2342 Planarity : 0.004 0.042 2093 Dihedral : 19.529 174.020 3200 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.30 % Allowed : 13.32 % Favored : 84.38 % 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: 1.74 (0.21), residues: 672 sheet: 0.61 (0.55), residues: 93 loop : -0.64 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.013 0.002 TYR B1013 PHE 0.012 0.002 PHE B 446 TRP 0.011 0.002 TRP B 659 HIS 0.007 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.25 (14747) covalent geometry : angle 0.73663 / 0.35 (20533) hydrogen bonds : bond 0.05099 / 5.53 ( 637) hydrogen bonds : angle 4.45478 / 5.95 ( 1709) *********************** 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 83 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8588 (mmp) cc_final: 0.7994 (mmp) REVERT: B 534 MET cc_start: 0.6155 (ttm) cc_final: 0.4913 (ptm) REVERT: B 613 GLU cc_start: 0.9676 (OUTLIER) cc_final: 0.9336 (tm-30) REVERT: B 703 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8826 (t) REVERT: B 727 LEU cc_start: 0.8669 (mt) cc_final: 0.8000 (mt) REVERT: B 801 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.4526 (p) REVERT: B 813 LEU cc_start: 0.9836 (mt) cc_final: 0.9632 (tp) REVERT: B 815 TYR cc_start: 0.9553 (m-80) cc_final: 0.9105 (m-80) REVERT: B 1021 MET cc_start: 0.8810 (mpp) cc_final: 0.8341 (mmp) REVERT: B 1043 MET cc_start: 0.8794 (tmm) cc_final: 0.8571 (tmm) REVERT: B 1099 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 1219 GLU cc_start: 0.8000 (tt0) cc_final: 0.7740 (mt-10) REVERT: B 1333 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8310 (ptt180) outliers start: 28 outliers final: 19 residues processed: 79 average time/residue: 0.1253 time to fit residues: 14.9989 Evaluate side-chains 75 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 96 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 141 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 7 optimal weight: 8.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 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 = 0.3345 r_free = 0.3345 target = 0.049008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.034741 restraints weight = 109351.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.036033 restraints weight = 53552.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.036741 restraints weight = 34962.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037225 restraints weight = 27562.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.037489 restraints weight = 23929.664| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14747 Z= 0.136 Angle : 0.677 13.399 20533 Z= 0.320 Chirality : 0.049 0.484 2342 Planarity : 0.003 0.041 2093 Dihedral : 19.427 173.880 3200 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.97 % Allowed : 13.82 % Favored : 84.21 % 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: 1.04 (0.23), residues: 1353 helix: 1.79 (0.21), residues: 673 sheet: 0.54 (0.54), residues: 93 loop : -0.57 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 895 TYR 0.012 0.001 TYR B1013 PHE 0.009 0.001 PHE B 446 TRP 0.006 0.001 TRP B 18 HIS 0.005 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (14747) covalent geometry : angle 0.67719 / 0.32 (20533) hydrogen bonds : bond 0.03914 / 4.24 ( 637) hydrogen bonds : angle 4.21362 / 5.67 ( 1709) *********************** 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: 24 poor density : 57 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9546 (mmm) cc_final: 0.9272 (mmm) REVERT: B 103 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8346 (pp20) REVERT: B 383 MET cc_start: 0.8549 (mmp) cc_final: 0.7949 (mmp) REVERT: B 534 MET cc_start: 0.6081 (ttm) cc_final: 0.4835 (ptm) REVERT: B 727 LEU cc_start: 0.8655 (mt) cc_final: 0.7985 (mt) REVERT: B 751 MET cc_start: 0.9031 (tpp) cc_final: 0.8563 (ttm) REVERT: B 801 VAL cc_start: 0.5045 (OUTLIER) cc_final: 0.4256 (p) REVERT: B 813 LEU cc_start: 0.9831 (mt) cc_final: 0.9611 (tp) REVERT: B 815 TYR cc_start: 0.9519 (m-80) cc_final: 0.9057 (m-80) REVERT: B 965 ASP cc_start: 0.9550 (OUTLIER) cc_final: 0.9061 (m-30) REVERT: B 1021 MET cc_start: 0.8783 (mpp) cc_final: 0.8229 (mpp) REVERT: B 1043 MET cc_start: 0.8748 (tmm) cc_final: 0.8543 (tmm) REVERT: B 1099 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 1213 MET cc_start: 0.6690 (mtp) cc_final: 0.6447 (tpp) REVERT: B 1219 GLU cc_start: 0.7873 (tt0) cc_final: 0.7135 (mt-10) REVERT: B 1333 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8330 (ptt180) REVERT: B 1350 GLN cc_start: 0.8888 (mt0) cc_final: 0.8626 (tt0) outliers start: 24 outliers final: 17 residues processed: 78 average time/residue: 0.1171 time to fit residues: 13.9762 Evaluate side-chains 73 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1348 ILE Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 134 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 113 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 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 = 0.3320 r_free = 0.3320 target = 0.048017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033862 restraints weight = 112100.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.035099 restraints weight = 54924.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.035827 restraints weight = 36067.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.036240 restraints weight = 28281.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036520 restraints weight = 24837.692| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14747 Z= 0.215 Angle : 0.723 13.936 20533 Z= 0.343 Chirality : 0.049 0.504 2342 Planarity : 0.004 0.043 2093 Dihedral : 19.516 174.180 3200 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.97 % Allowed : 14.14 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1353 helix: 1.74 (0.21), residues: 672 sheet: 0.60 (0.55), residues: 93 loop : -0.56 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.012 0.001 TYR B 5 PHE 0.011 0.001 PHE B 446 TRP 0.009 0.002 TRP B 476 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (14747) covalent geometry : angle 0.72333 / 0.34 (20533) hydrogen bonds : bond 0.04842 / 5.24 ( 637) hydrogen bonds : angle 4.39790 / 5.88 ( 1709) *********************** 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 76 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9550 (mmm) cc_final: 0.9327 (mmm) REVERT: B 383 MET cc_start: 0.8611 (mmp) cc_final: 0.7994 (mmp) REVERT: B 517 TYR cc_start: 0.9457 (m-80) cc_final: 0.9213 (m-80) REVERT: B 534 MET cc_start: 0.6091 (ttm) cc_final: 0.4907 (ptm) REVERT: B 613 GLU cc_start: 0.9672 (OUTLIER) cc_final: 0.9323 (tm-30) REVERT: B 727 LEU cc_start: 0.8669 (mt) cc_final: 0.8028 (mt) REVERT: B 801 VAL cc_start: 0.5103 (OUTLIER) cc_final: 0.4478 (p) REVERT: B 813 LEU cc_start: 0.9843 (mt) cc_final: 0.9633 (tp) REVERT: B 815 TYR cc_start: 0.9537 (m-80) cc_final: 0.9082 (m-80) REVERT: B 1021 MET cc_start: 0.8820 (mpp) cc_final: 0.8289 (mpp) REVERT: B 1043 MET cc_start: 0.8788 (tmm) cc_final: 0.8579 (tmm) REVERT: B 1099 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 1219 GLU cc_start: 0.7917 (tt0) cc_final: 0.7650 (mt-10) REVERT: B 1333 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8286 (ptt180) outliers start: 24 outliers final: 18 residues processed: 73 average time/residue: 0.1085 time to fit residues: 12.5327 Evaluate side-chains 73 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 0.0970 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 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 = 0.3348 r_free = 0.3348 target = 0.048961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.034691 restraints weight = 110021.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.035975 restraints weight = 53699.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036748 restraints weight = 35066.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.037172 restraints weight = 27355.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037360 restraints weight = 23913.729| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 14747 Z= 0.122 Angle : 0.682 16.691 20533 Z= 0.323 Chirality : 0.049 0.477 2342 Planarity : 0.003 0.042 2093 Dihedral : 19.379 174.034 3200 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.56 % Allowed : 14.64 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1353 helix: 1.79 (0.21), residues: 672 sheet: 0.57 (0.56), residues: 88 loop : -0.50 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 70 TYR 0.020 0.001 TYR B 451 PHE 0.008 0.001 PHE B 446 TRP 0.007 0.001 TRP B 18 HIS 0.006 0.001 HIS B1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14747) covalent geometry : angle 0.68159 / 0.32 (20533) hydrogen bonds : bond 0.03808 / 4.11 ( 637) hydrogen bonds : angle 4.17868 / 5.64 ( 1709) ********************** 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 76 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.517 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 90 MET cc_start: 0.9534 (mmm) cc_final: 0.9224 (mmm) REVERT: B 103 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8316 (pp20) REVERT: B 174 LEU cc_start: 0.9158 (pp) cc_final: 0.8735 (tp) REVERT: B 383 MET cc_start: 0.8564 (mmp) cc_final: 0.7934 (mmp) REVERT: B 534 MET cc_start: 0.6078 (ttm) cc_final: 0.4866 (ptm) REVERT: B 727 LEU cc_start: 0.8655 (mt) cc_final: 0.8130 (mt) REVERT: B 801 VAL cc_start: 0.5162 (OUTLIER) cc_final: 0.4508 (p) REVERT: B 815 TYR cc_start: 0.9501 (m-80) cc_final: 0.9019 (m-80) REVERT: B 1021 MET cc_start: 0.8767 (mpp) cc_final: 0.8267 (mpp) REVERT: B 1099 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 1219 GLU cc_start: 0.7819 (tt0) cc_final: 0.7073 (mt-10) REVERT: B 1333 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8303 (ptt180) outliers start: 19 outliers final: 15 residues processed: 73 average time/residue: 0.1145 time to fit residues: 13.1538 Evaluate side-chains 71 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1010 TYR Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 0.0270 overall best weight: 6.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 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 = 0.3303 r_free = 0.3303 target = 0.047501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.033267 restraints weight = 113514.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.034482 restraints weight = 55975.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.035165 restraints weight = 36807.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.035643 restraints weight = 29116.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.035884 restraints weight = 25267.227| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14747 Z= 0.288 Angle : 0.790 13.619 20533 Z= 0.375 Chirality : 0.050 0.535 2342 Planarity : 0.004 0.048 2093 Dihedral : 19.556 174.166 3199 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.64 % Allowed : 15.05 % Favored : 83.31 % 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: 0.90 (0.23), residues: 1353 helix: 1.60 (0.21), residues: 672 sheet: 0.63 (0.56), residues: 93 loop : -0.56 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 165 TYR 0.043 0.002 TYR B 451 PHE 0.014 0.002 PHE B 462 TRP 0.012 0.002 TRP B 476 HIS 0.007 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.29 (14747) covalent geometry : angle 0.78966 / 0.38 (20533) hydrogen bonds : bond 0.05445 / 5.88 ( 637) hydrogen bonds : angle 4.54597 / 6.07 ( 1709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.57 seconds wall clock time: 44 minutes 16.43 seconds (2656.43 seconds total)