Starting phenix.real_space_refine on Sat Sep 12 02:02:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4g_14496/09_2026/7z4g_14496.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 140 5.49 5 S 19 5.16 5 C 7585 2.51 5 N 2223 2.21 5 O 2747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12714 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1932 Classifications: {'DNA': 1, 'RNAv2': 90} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 78} 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: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9711 Classifications: {'peptide': 1188} Link IDs: {'PTRANS': 32, 'TRANS': 1155} Chain breaks: 4 Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 625 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Inner-chain residues flagged as termini: ['pdbres=" DA D -2 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 21} Time building chain proxies: 2.73, per 1000 atoms: 0.21 Number of scatterers: 12714 At special positions: 0 Unit cell: (86.45, 130, 122.85, 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 19 16.00 P 140 15.00 O 2747 8.00 N 2223 7.00 C 7585 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: 1.20 Conformation dependent library (CDL) restraints added in 429.9 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 10 sheets defined 55.3% alpha, 9.1% beta 53 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.569A pdb=" N LYS B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) 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 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.553A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.332A pdb=" N ASN B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.983A pdb=" N ASP B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.585A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (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 387 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.869A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.117A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 removed outlier: 3.556A pdb=" N ILE B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 526 removed outlier: 4.146A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.567A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.520A pdb=" N THR B 622 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 712 removed outlier: 4.241A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.796A pdb=" N LYS B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.879A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.112A 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 1076 through 1088 removed outlier: 3.905A pdb=" N PHE B1080 " --> pdb=" O LYS B1076 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA B1081 " --> pdb=" O GLY B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1185 removed outlier: 3.561A pdb=" N LYS B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1241 removed outlier: 3.570A pdb=" N HIS B1241 " --> pdb=" O TYR B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1264 Processing helix chain 'B' and resid 1265 through 1280 removed outlier: 3.652A pdb=" N ILE B1269 " --> pdb=" O TYR B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 958 removed outlier: 6.296A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 958 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 761 " --> pdb=" O LEU B 958 " (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 507 through 509 removed outlier: 5.485A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.847A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 528 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 581 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA7, first strand: chain 'B' and resid 1107 through 1111 removed outlier: 6.909A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.557A pdb=" N LYS B1158 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1149 " --> pdb=" O LYS B1158 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B1196 " --> pdb=" O LEU B1144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1219 through 1222 removed outlier: 6.249A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 457 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.57 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: 2820 1.33 - 1.45: 3374 1.45 - 1.57: 6738 1.57 - 1.69: 281 1.69 - 1.81: 36 Bond restraints: 13249 Sorted by residual: bond pdb=" C3' DG C 1 " pdb=" C2' DG C 1 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.38e+00 bond pdb=" C3' DC C 2 " pdb=" C2' DC C 2 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.29e+00 bond pdb=" C1' DT C 9 " pdb=" N1 DT C 9 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.45e+00 bond pdb=" C3' DG D 1 " pdb=" C2' DG D 1 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.04e+00 bond pdb=" C3' DA C 8 " pdb=" O3' DA C 8 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.67e+00 ... (remaining 13244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 17730 1.43 - 2.86: 620 2.86 - 4.28: 128 4.28 - 5.71: 23 5.71 - 7.14: 1 Bond angle restraints: 18502 Sorted by residual: angle pdb=" O4' DG D -16 " pdb=" C4' DG D -16 " pdb=" C3' DG D -16 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.15e+01 angle pdb=" O4' DG C 3 " pdb=" C4' DG C 3 " pdb=" C3' DG C 3 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" O4' DT C 9 " pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.09e+01 angle pdb=" O4' DC D -17 " pdb=" C4' DC D -17 " pdb=" C3' DC D -17 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+01 ... (remaining 18497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 6781 16.32 - 32.63: 507 32.63 - 48.95: 243 48.95 - 65.26: 156 65.26 - 81.58: 18 Dihedral angle restraints: 7705 sinusoidal: 4212 harmonic: 3493 Sorted by residual: dihedral pdb=" C4' U A 63 " pdb=" C3' U A 63 " pdb=" C2' U A 63 " pdb=" C1' U A 63 " ideal model delta sinusoidal sigma weight residual 36.34 -36.54 72.89 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' U A 44 " pdb=" C3' U A 44 " pdb=" C2' U A 44 " pdb=" C1' U A 44 " ideal model delta sinusoidal sigma weight residual 36.35 -36.48 72.83 1 3.10e+00 1.04e-01 7.04e+02 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 -36.30 72.64 1 3.10e+00 1.04e-01 7.01e+02 ... (remaining 7702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1771 0.058 - 0.116: 226 0.116 - 0.174: 16 0.174 - 0.231: 66 0.231 - 0.289: 49 Chirality restraints: 2128 Sorted by residual: chirality pdb=" P G A 95 " pdb=" OP1 G A 95 " pdb=" OP2 G A 95 " pdb=" O5' G A 95 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.09e+00 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 -2.50 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' A A 28 " pdb=" C3' A A 28 " pdb=" O2' A A 28 " pdb=" C1' A A 28 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2125 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 993 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL B 993 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B 993 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 994 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 991 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ALA B 991 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 991 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 992 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 83 " -0.025 2.00e-02 2.50e+03 1.39e-02 4.36e+00 pdb=" N1 C A 83 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C A 83 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 83 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C A 83 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A 83 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C A 83 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C A 83 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C A 83 " 0.003 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1550 2.75 - 3.29: 12666 3.29 - 3.82: 23604 3.82 - 4.36: 27947 4.36 - 4.90: 42620 Nonbonded interactions: 108387 Sorted by model distance: nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.209 3.040 nonbonded pdb=" O2' G A 58 " pdb=" O LEU B 455 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS B 140 " pdb=" OD2 ASP B 144 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS B1161 " pdb=" OD1 ASP B1344 " model vdw 2.210 3.120 nonbonded pdb=" O GLU B1304 " pdb=" ND2 ASN B1308 " model vdw 2.219 3.120 ... (remaining 108382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.580 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13249 Z= 0.260 Angle : 0.632 7.138 18502 Z= 0.399 Chirality : 0.066 0.289 2128 Planarity : 0.004 0.034 1842 Dihedral : 16.182 81.578 5441 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.03 % Allowed : 4.89 % Favored : 94.08 % 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: 1.30 (0.25), residues: 1178 helix: 1.99 (0.23), residues: 590 sheet: -0.09 (0.61), residues: 78 loop : -0.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 654 TYR 0.015 0.001 TYR B1001 PHE 0.012 0.001 PHE B 462 TRP 0.011 0.001 TRP B 464 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.26 (13249) covalent geometry : angle 0.63155 / 0.40 (18502) hydrogen bonds : bond 0.12206 / 6.20 ( 590) hydrogen bonds : angle 5.78352 / 2.38 ( 1588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8968 (tptt) REVERT: B 80 CYS cc_start: 0.8333 (m) cc_final: 0.8093 (m) REVERT: B 90 MET cc_start: 0.7978 (tpp) cc_final: 0.7648 (tpt) REVERT: B 100 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.7821 (mtm-85) REVERT: B 151 LEU cc_start: 0.8537 (tp) cc_final: 0.8082 (pt) REVERT: B 534 MET cc_start: 0.8219 (mtp) cc_final: 0.6952 (ppp) REVERT: B 569 PHE cc_start: 0.9358 (m-80) cc_final: 0.9078 (m-80) REVERT: B 593 THR cc_start: 0.8038 (m) cc_final: 0.7803 (p) REVERT: B 625 LEU cc_start: 0.8289 (mt) cc_final: 0.8084 (mt) REVERT: B 723 HIS cc_start: 0.9258 (t70) cc_final: 0.8924 (m90) REVERT: B 1043 MET cc_start: 0.6177 (ttp) cc_final: 0.5707 (tmm) REVERT: B 1170 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8550 (mm-30) REVERT: B 1266 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9019 (tp) REVERT: B 1268 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8705 (mp0) outliers start: 11 outliers final: 2 residues processed: 222 average time/residue: 0.1369 time to fit residues: 41.3541 Evaluate side-chains 114 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1266 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 329 HIS B 497 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS B 721 HIS ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B1101 GLN ** B1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.070798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.056351 restraints weight = 79122.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.058027 restraints weight = 42852.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.059105 restraints weight = 28459.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.059807 restraints weight = 21781.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.060285 restraints weight = 18318.517| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 13249 Z= 0.343 Angle : 1.089 25.354 18502 Z= 0.493 Chirality : 0.082 1.204 2128 Planarity : 0.006 0.094 1842 Dihedral : 17.984 126.917 2938 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.67 % Allowed : 11.84 % Favored : 84.49 % 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: 0.83 (0.24), residues: 1178 helix: 1.40 (0.21), residues: 595 sheet: 0.19 (0.61), residues: 76 loop : -0.35 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 494 TYR 0.025 0.002 TYR B1265 PHE 0.025 0.003 PHE B1046 TRP 0.013 0.002 TRP B 464 HIS 0.007 0.002 HIS B1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.34 (13249) covalent geometry : angle 1.08868 / 0.49 (18502) hydrogen bonds : bond 0.05985 / 3.15 ( 590) hydrogen bonds : angle 5.36237 / 2.21 ( 1588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8949 (tptt) REVERT: B 80 CYS cc_start: 0.8389 (m) cc_final: 0.8114 (m) REVERT: B 100 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8524 (mtp180) REVERT: B 464 TRP cc_start: 0.7107 (p90) cc_final: 0.6884 (p90) REVERT: B 534 MET cc_start: 0.7813 (mtp) cc_final: 0.5531 (mtp) REVERT: B 569 PHE cc_start: 0.9404 (m-80) cc_final: 0.9012 (m-80) REVERT: B 645 ASP cc_start: 0.9101 (p0) cc_final: 0.8427 (p0) REVERT: B 649 LYS cc_start: 0.9308 (ttmt) cc_final: 0.9105 (ptpp) REVERT: B 682 PHE cc_start: 0.8734 (m-80) cc_final: 0.8323 (m-10) REVERT: B 723 HIS cc_start: 0.9559 (t70) cc_final: 0.9095 (m170) REVERT: B 933 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.9262 (tp-100) REVERT: B 1043 MET cc_start: 0.6232 (ttp) cc_final: 0.5809 (tmm) REVERT: B 1170 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8664 (mt-10) outliers start: 39 outliers final: 19 residues processed: 132 average time/residue: 0.1244 time to fit residues: 23.2359 Evaluate side-chains 110 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 933 GLN Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B1261 GLN B1272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.058393 restraints weight = 76510.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.060146 restraints weight = 41262.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061292 restraints weight = 27110.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.061973 restraints weight = 20476.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.062541 restraints weight = 17266.963| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13249 Z= 0.166 Angle : 0.796 14.399 18502 Z= 0.372 Chirality : 0.062 0.890 2128 Planarity : 0.004 0.093 1842 Dihedral : 18.062 153.403 2936 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.01 % Allowed : 12.03 % Favored : 84.96 % 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: 1.03 (0.24), residues: 1178 helix: 1.62 (0.22), residues: 596 sheet: 0.23 (0.60), residues: 76 loop : -0.34 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 535 TYR 0.027 0.002 TYR B1265 PHE 0.010 0.001 PHE B1046 TRP 0.011 0.001 TRP B 464 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (13249) covalent geometry : angle 0.79646 / 0.37 (18502) hydrogen bonds : bond 0.04346 / 2.26 ( 590) hydrogen bonds : angle 4.86743 / 2.03 ( 1588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8855 (tptt) REVERT: B 80 CYS cc_start: 0.8255 (m) cc_final: 0.7994 (m) REVERT: B 682 PHE cc_start: 0.8559 (m-80) cc_final: 0.8237 (m-80) REVERT: B 723 HIS cc_start: 0.9589 (t70) cc_final: 0.9072 (m90) REVERT: B 1043 MET cc_start: 0.6091 (ttp) cc_final: 0.5589 (tmm) REVERT: B 1253 GLU cc_start: 0.9457 (tp30) cc_final: 0.8934 (mm-30) REVERT: B 1357 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8670 (mp0) outliers start: 32 outliers final: 20 residues processed: 123 average time/residue: 0.1061 time to fit residues: 19.3030 Evaluate side-chains 112 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 953 VAL Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 HIS B1101 GLN B1261 GLN B1272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.067856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.053592 restraints weight = 80562.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.055132 restraints weight = 43995.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.056149 restraints weight = 29674.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.056835 restraints weight = 22893.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.057234 restraints weight = 19248.386| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 13249 Z= 0.399 Angle : 1.012 13.471 18502 Z= 0.476 Chirality : 0.063 0.771 2128 Planarity : 0.007 0.111 1842 Dihedral : 18.087 155.100 2934 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.23 % Allowed : 13.72 % Favored : 82.05 % 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: 0.14 (0.24), residues: 1178 helix: 0.84 (0.21), residues: 600 sheet: -0.42 (0.53), residues: 85 loop : -0.66 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 557 TYR 0.033 0.003 TYR B1242 PHE 0.025 0.003 PHE B1235 TRP 0.035 0.003 TRP B 464 HIS 0.010 0.002 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.40 (13249) covalent geometry : angle 1.01171 / 0.48 (18502) hydrogen bonds : bond 0.07180 / 3.74 ( 590) hydrogen bonds : angle 5.55621 / 2.28 ( 1588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 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 65 LYS cc_start: 0.9220 (mmtt) cc_final: 0.8950 (tptt) REVERT: B 80 CYS cc_start: 0.8399 (m) cc_final: 0.8120 (m) REVERT: B 101 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8587 (mp) REVERT: B 569 PHE cc_start: 0.9489 (m-80) cc_final: 0.9036 (m-80) REVERT: B 645 ASP cc_start: 0.9156 (p0) cc_final: 0.8940 (p0) REVERT: B 723 HIS cc_start: 0.9619 (t70) cc_final: 0.9077 (m170) REVERT: B 933 GLN cc_start: 0.9559 (OUTLIER) cc_final: 0.9190 (tp-100) REVERT: B 1043 MET cc_start: 0.5924 (ttp) cc_final: 0.5470 (tmm) outliers start: 45 outliers final: 29 residues processed: 115 average time/residue: 0.1031 time to fit residues: 18.1315 Evaluate side-chains 109 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 933 GLN Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1135 ASP Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1302 ILE Chi-restraints excluded: chain B residue 1316 THR Chi-restraints excluded: chain B residue 1331 ILE Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 129 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 104 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.070310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.055954 restraints weight = 77321.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.057612 restraints weight = 41477.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.058686 restraints weight = 27441.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.059367 restraints weight = 20864.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.059890 restraints weight = 17539.843| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13249 Z= 0.182 Angle : 0.774 11.612 18502 Z= 0.366 Chirality : 0.058 0.774 2128 Planarity : 0.005 0.093 1842 Dihedral : 17.901 149.274 2934 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.10 % Allowed : 14.85 % Favored : 82.05 % 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: 0.60 (0.24), residues: 1178 helix: 1.23 (0.21), residues: 597 sheet: -0.07 (0.57), residues: 76 loop : -0.47 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 976 TYR 0.022 0.002 TYR B1242 PHE 0.018 0.001 PHE B1046 TRP 0.022 0.002 TRP B 464 HIS 0.011 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (13249) covalent geometry : angle 0.77387 / 0.37 (18502) hydrogen bonds : bond 0.04689 / 2.45 ( 590) hydrogen bonds : angle 4.95576 / 2.06 ( 1588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.296 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 65 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8882 (tptt) REVERT: B 80 CYS cc_start: 0.8234 (m) cc_final: 0.7962 (m) REVERT: B 569 PHE cc_start: 0.9398 (m-80) cc_final: 0.8975 (m-80) REVERT: B 645 ASP cc_start: 0.9151 (p0) cc_final: 0.8726 (t0) REVERT: B 723 HIS cc_start: 0.9610 (t70) cc_final: 0.9078 (m170) REVERT: B 755 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8286 (ptmm) REVERT: B 1043 MET cc_start: 0.5748 (ttp) cc_final: 0.5353 (tmm) outliers start: 33 outliers final: 26 residues processed: 108 average time/residue: 0.1061 time to fit residues: 17.2823 Evaluate side-chains 106 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 chunk 114 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.072449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.058012 restraints weight = 75917.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.059783 restraints weight = 39974.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.060841 restraints weight = 26017.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.061660 restraints weight = 19788.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.062125 restraints weight = 16278.069| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13249 Z= 0.136 Angle : 0.713 12.974 18502 Z= 0.341 Chirality : 0.054 0.698 2128 Planarity : 0.004 0.079 1842 Dihedral : 17.689 144.925 2934 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.16 % Allowed : 15.98 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1178 helix: 1.37 (0.21), residues: 598 sheet: 0.02 (0.56), residues: 78 loop : -0.33 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 629 TYR 0.022 0.001 TYR B 271 PHE 0.013 0.001 PHE B1046 TRP 0.010 0.001 TRP B 464 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (13249) covalent geometry : angle 0.71278 / 0.34 (18502) hydrogen bonds : bond 0.04047 / 2.14 ( 590) hydrogen bonds : angle 4.65281 / 1.94 ( 1588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.434 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 65 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8856 (mmmt) REVERT: B 80 CYS cc_start: 0.8270 (m) cc_final: 0.7989 (m) REVERT: B 161 MET cc_start: 0.8070 (ptp) cc_final: 0.6910 (ptp) REVERT: B 271 TYR cc_start: 0.8592 (t80) cc_final: 0.8376 (t80) REVERT: B 383 MET cc_start: 0.8896 (tpp) cc_final: 0.8677 (tpp) REVERT: B 495 MET cc_start: 0.6557 (ptp) cc_final: 0.6188 (mtm) REVERT: B 569 PHE cc_start: 0.9392 (m-80) cc_final: 0.8991 (m-80) REVERT: B 694 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8548 (mpp) REVERT: B 723 HIS cc_start: 0.9602 (t70) cc_final: 0.9076 (m170) REVERT: B 755 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8341 (ptmm) REVERT: B 1043 MET cc_start: 0.5606 (ttp) cc_final: 0.5186 (tmm) REVERT: B 1253 GLU cc_start: 0.9457 (tp30) cc_final: 0.8964 (mm-30) outliers start: 23 outliers final: 16 residues processed: 107 average time/residue: 0.1000 time to fit residues: 16.5628 Evaluate side-chains 100 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 130 optimal weight: 50.0000 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.071487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.056917 restraints weight = 76236.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.058639 restraints weight = 39979.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.059764 restraints weight = 26249.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.060458 restraints weight = 19860.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.060982 restraints weight = 16707.788| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13249 Z= 0.170 Angle : 0.728 12.002 18502 Z= 0.347 Chirality : 0.053 0.669 2128 Planarity : 0.004 0.069 1842 Dihedral : 17.735 145.894 2934 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 16.26 % Favored : 81.20 % 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: 0.87 (0.25), residues: 1178 helix: 1.46 (0.21), residues: 599 sheet: -0.12 (0.57), residues: 78 loop : -0.33 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 629 TYR 0.025 0.001 TYR B 271 PHE 0.017 0.001 PHE B 518 TRP 0.008 0.001 TRP B 464 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (13249) covalent geometry : angle 0.72778 / 0.35 (18502) hydrogen bonds : bond 0.04289 / 2.26 ( 590) hydrogen bonds : angle 4.66907 / 1.93 ( 1588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9191 (mmtt) cc_final: 0.8852 (tptt) REVERT: B 80 CYS cc_start: 0.8325 (m) cc_final: 0.8020 (m) REVERT: B 218 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8894 (ptmt) REVERT: B 383 MET cc_start: 0.8783 (tpp) cc_final: 0.8214 (tpp) REVERT: B 534 MET cc_start: 0.4244 (ptt) cc_final: 0.3852 (ptt) REVERT: B 569 PHE cc_start: 0.9424 (m-80) cc_final: 0.9028 (m-80) REVERT: B 645 ASP cc_start: 0.9237 (p0) cc_final: 0.8847 (t0) REVERT: B 694 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8516 (mpp) REVERT: B 723 HIS cc_start: 0.9619 (t70) cc_final: 0.9334 (t-90) REVERT: B 755 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8358 (ptmm) REVERT: B 1043 MET cc_start: 0.5557 (ttp) cc_final: 0.5163 (tmm) REVERT: B 1108 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8770 (mp0) outliers start: 27 outliers final: 20 residues processed: 98 average time/residue: 0.1043 time to fit residues: 15.6359 Evaluate side-chains 102 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1213 MET Chi-restraints excluded: chain B residue 1265 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 26 optimal weight: 0.0670 overall best weight: 4.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.069652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.055187 restraints weight = 76757.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.056851 restraints weight = 40343.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.057926 restraints weight = 26635.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.058547 restraints weight = 20248.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.059052 restraints weight = 17184.605| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 13249 Z= 0.246 Angle : 0.785 11.345 18502 Z= 0.375 Chirality : 0.055 0.730 2128 Planarity : 0.005 0.067 1842 Dihedral : 17.842 148.577 2934 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.38 % Allowed : 16.07 % Favored : 80.55 % 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: 0.64 (0.25), residues: 1178 helix: 1.28 (0.21), residues: 601 sheet: -0.32 (0.58), residues: 78 loop : -0.45 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 629 TYR 0.026 0.002 TYR B 271 PHE 0.017 0.002 PHE B1235 TRP 0.017 0.002 TRP B 464 HIS 0.010 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.25 (13249) covalent geometry : angle 0.78501 / 0.37 (18502) hydrogen bonds : bond 0.05106 / 2.68 ( 590) hydrogen bonds : angle 4.88619 / 2.02 ( 1588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.435 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 65 LYS cc_start: 0.9230 (mmtt) cc_final: 0.8919 (tptt) REVERT: B 80 CYS cc_start: 0.8413 (m) cc_final: 0.8098 (m) REVERT: B 218 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8925 (ptmt) REVERT: B 534 MET cc_start: 0.4376 (ptt) cc_final: 0.3985 (ptt) REVERT: B 569 PHE cc_start: 0.9463 (m-80) cc_final: 0.9063 (m-80) REVERT: B 645 ASP cc_start: 0.9241 (p0) cc_final: 0.8618 (t0) REVERT: B 723 HIS cc_start: 0.9622 (t70) cc_final: 0.9348 (t-90) REVERT: B 755 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8378 (ptmm) REVERT: B 933 GLN cc_start: 0.9573 (tp-100) cc_final: 0.9080 (tp-100) REVERT: B 1043 MET cc_start: 0.5596 (ttp) cc_final: 0.5195 (tmm) outliers start: 36 outliers final: 27 residues processed: 104 average time/residue: 0.1024 time to fit residues: 16.2751 Evaluate side-chains 102 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1302 ILE Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 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 = 0.3762 r_free = 0.3762 target = 0.069193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.054816 restraints weight = 77584.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.056467 restraints weight = 41148.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.057518 restraints weight = 27212.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.058213 restraints weight = 20782.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.058524 restraints weight = 17337.418| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13249 Z= 0.235 Angle : 0.791 11.757 18502 Z= 0.379 Chirality : 0.056 0.766 2128 Planarity : 0.005 0.066 1842 Dihedral : 17.880 148.715 2934 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.82 % Allowed : 16.92 % Favored : 80.26 % 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: 0.50 (0.25), residues: 1178 helix: 1.16 (0.21), residues: 599 sheet: -0.52 (0.55), residues: 87 loop : -0.45 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 629 TYR 0.034 0.002 TYR B 271 PHE 0.014 0.002 PHE B1235 TRP 0.009 0.002 TRP B 464 HIS 0.010 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (13249) covalent geometry : angle 0.79104 / 0.38 (18502) hydrogen bonds : bond 0.05069 / 2.67 ( 590) hydrogen bonds : angle 4.94205 / 2.04 ( 1588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.461 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 65 LYS cc_start: 0.9197 (mmtt) cc_final: 0.8884 (tptt) REVERT: B 80 CYS cc_start: 0.8387 (m) cc_final: 0.8087 (m) REVERT: B 101 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 495 MET cc_start: 0.6979 (ptt) cc_final: 0.6298 (ptm) REVERT: B 534 MET cc_start: 0.4464 (ptt) cc_final: 0.4023 (ptt) REVERT: B 569 PHE cc_start: 0.9467 (m-80) cc_final: 0.9073 (m-80) REVERT: B 645 ASP cc_start: 0.9301 (p0) cc_final: 0.8871 (t0) REVERT: B 648 MET cc_start: 0.9216 (tmm) cc_final: 0.8984 (mtt) REVERT: B 723 HIS cc_start: 0.9619 (t70) cc_final: 0.9344 (t-90) REVERT: B 755 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8382 (ptmt) REVERT: B 1043 MET cc_start: 0.5629 (ttp) cc_final: 0.5248 (tmm) outliers start: 30 outliers final: 25 residues processed: 93 average time/residue: 0.1061 time to fit residues: 15.0959 Evaluate side-chains 99 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1302 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.071091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056596 restraints weight = 76651.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.058313 restraints weight = 39631.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.059437 restraints weight = 25864.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.060179 restraints weight = 19642.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.060602 restraints weight = 16329.521| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13249 Z= 0.143 Angle : 0.730 13.244 18502 Z= 0.348 Chirality : 0.053 0.692 2128 Planarity : 0.004 0.063 1842 Dihedral : 17.743 145.771 2934 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.35 % Allowed : 17.20 % Favored : 80.45 % 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: 0.76 (0.25), residues: 1178 helix: 1.29 (0.21), residues: 599 sheet: -0.24 (0.57), residues: 88 loop : -0.24 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 629 TYR 0.031 0.002 TYR B 271 PHE 0.013 0.001 PHE B1008 TRP 0.006 0.001 TRP B 476 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (13249) covalent geometry : angle 0.72958 / 0.35 (18502) hydrogen bonds : bond 0.04223 / 2.22 ( 590) hydrogen bonds : angle 4.65393 / 1.93 ( 1588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.431 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 65 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8821 (mmmt) REVERT: B 80 CYS cc_start: 0.8321 (m) cc_final: 0.8018 (m) REVERT: B 101 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 383 MET cc_start: 0.8498 (tpp) cc_final: 0.7809 (tpp) REVERT: B 534 MET cc_start: 0.4465 (ptt) cc_final: 0.3999 (ptt) REVERT: B 569 PHE cc_start: 0.9435 (m-80) cc_final: 0.9048 (m-80) REVERT: B 645 ASP cc_start: 0.9289 (p0) cc_final: 0.8331 (t0) REVERT: B 648 MET cc_start: 0.9157 (tmm) cc_final: 0.8585 (ppp) REVERT: B 723 HIS cc_start: 0.9575 (t70) cc_final: 0.9324 (t-90) REVERT: B 755 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8186 (ptmm) REVERT: B 1043 MET cc_start: 0.5529 (ttp) cc_final: 0.5146 (tmm) REVERT: B 1108 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8732 (mp0) outliers start: 25 outliers final: 21 residues processed: 95 average time/residue: 0.1011 time to fit residues: 15.0064 Evaluate side-chains 94 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1265 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.0370 chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 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 = 0.3782 r_free = 0.3782 target = 0.070228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055754 restraints weight = 77190.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.057451 restraints weight = 40182.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.058539 restraints weight = 26364.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.059261 restraints weight = 20069.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.059686 restraints weight = 16724.977| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13249 Z= 0.172 Angle : 0.740 13.350 18502 Z= 0.355 Chirality : 0.053 0.669 2128 Planarity : 0.004 0.057 1842 Dihedral : 17.737 146.818 2934 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.63 % Allowed : 17.48 % Favored : 79.89 % 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: 0.76 (0.25), residues: 1178 helix: 1.31 (0.22), residues: 600 sheet: -0.30 (0.58), residues: 88 loop : -0.26 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 629 TYR 0.029 0.002 TYR B 271 PHE 0.017 0.001 PHE B 518 TRP 0.006 0.001 TRP B 18 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (13249) covalent geometry : angle 0.73996 / 0.35 (18502) hydrogen bonds : bond 0.04510 / 2.37 ( 590) hydrogen bonds : angle 4.70458 / 1.94 ( 1588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.60 seconds wall clock time: 41 minutes 1.52 seconds (2461.52 seconds total)