Starting phenix.real_space_refine on Fri Jul 3 08:03:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4g_14496/07_2026/7z4g_14496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4g_14496/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2026/7z4g_14496.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2026/7z4g_14496.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2026/7z4g_14496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2026/7z4g_14496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2026/7z4g_14496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2026/7z4g_14496.map" } 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-dev-6108/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, 'RNA': 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: 2 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: 2.77, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 350.0 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: 1.79 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: 3.31 Time building geometry restraints manager: 1.10 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: 17992 1.43 - 2.86: 461 2.86 - 4.28: 48 4.28 - 5.71: 3 5.71 - 7.14: 1 Bond angle restraints: 18505 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 18500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 6969 17.09 - 34.18: 465 34.18 - 51.27: 196 51.27 - 68.35: 70 68.35 - 85.44: 6 Dihedral angle restraints: 7706 sinusoidal: 4213 harmonic: 3493 Sorted by residual: dihedral pdb=" CA LYS B1263 " pdb=" C LYS B1263 " pdb=" N HIS B1264 " pdb=" CA HIS B1264 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CG ARG B 753 " pdb=" CD ARG B 753 " pdb=" NE ARG B 753 " pdb=" CZ ARG B 753 " ideal model delta sinusoidal sigma weight residual 180.00 135.51 44.49 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" O5' U A 44 " pdb=" C5' U A 44 " pdb=" C4' U A 44 " pdb=" C3' U A 44 " ideal model delta sinusoidal sigma weight residual -65.00 -5.23 -59.77 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 7703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1738 0.046 - 0.092: 309 0.092 - 0.137: 77 0.137 - 0.183: 3 0.183 - 0.229: 1 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA ARG B 753 " pdb=" N ARG B 753 " pdb=" C ARG B 753 " pdb=" CB ARG B 753 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE B 956 " pdb=" N ILE B 956 " pdb=" C ILE B 956 " pdb=" CB ILE B 956 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" C1' A A 42 " pdb=" O4' A A 42 " pdb=" C2' A A 42 " pdb=" N9 A A 42 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.34e-01 ... (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: 4.790 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: 14.040 Find NCS groups from input model: 0.180 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- 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= 0.256 Angle : 0.521 7.138 18505 Z= 0.380 Chirality : 0.037 0.229 2128 Planarity : 0.004 0.034 1842 Dihedral : 14.024 85.443 5442 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 0.00352 / 0.26 (13249) covalent geometry : angle 0.52084 / 0.38 (18505) hydrogen bonds : bond 0.12206 / 7.08 ( 590) hydrogen bonds : angle 5.78352 / 3.35 ( 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 : 0.370 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: 0.1345 time to fit residues: 40.4423 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 : 0.308 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.070730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.056191 restraints weight = 78853.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.057866 restraints weight = 42564.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.058876 restraints weight = 28258.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.059589 restraints weight = 21807.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.060133 restraints weight = 18387.758| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13249 Z= 0.311 Angle : 0.738 9.127 18505 Z= 0.399 Chirality : 0.043 0.240 2128 Planarity : 0.006 0.090 1842 Dihedral : 15.910 85.200 2939 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.85 % Allowed : 11.75 % Favored : 84.40 % 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: 0.73 (0.24), residues: 1178 helix: 1.31 (0.21), residues: 595 sheet: 0.15 (0.61), residues: 76 loop : -0.39 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 494 TYR 0.026 0.002 TYR B1265 PHE 0.029 0.003 PHE B1046 TRP 0.017 0.002 TRP B 464 HIS 0.010 0.002 HIS B 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.31 (13249) covalent geometry : angle 0.73824 / 0.40 (18505) hydrogen bonds : bond 0.06023 / 3.50 ( 590) hydrogen bonds : angle 5.38359 / 3.01 ( 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 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.465 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: B 65 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8975 (tptt) REVERT: B 80 CYS cc_start: 0.8369 (m) cc_final: 0.8107 (m) REVERT: B 100 ARG cc_start: 0.8779 (mtm-85) cc_final: 0.8496 (mtp180) REVERT: B 464 TRP cc_start: 0.7112 (p90) cc_final: 0.6896 (p90) REVERT: B 534 MET cc_start: 0.7685 (mtp) cc_final: 0.5458 (mtp) REVERT: B 569 PHE cc_start: 0.9387 (m-80) cc_final: 0.8999 (m-80) REVERT: B 682 PHE cc_start: 0.8720 (m-80) cc_final: 0.8330 (m-10) REVERT: B 722 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9029 (pp20) REVERT: B 933 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.9252 (tp-100) REVERT: B 1043 MET cc_start: 0.6215 (ttp) cc_final: 0.5814 (tmm) REVERT: B 1089 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8607 (mtt) REVERT: B 1170 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8655 (mt-10) outliers start: 41 outliers final: 22 residues processed: 134 average time/residue: 0.1313 time to fit residues: 24.8435 Evaluate side-chains 114 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 974 LYS Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1274 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.071249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.056831 restraints weight = 77357.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.058516 restraints weight = 41543.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.059651 restraints weight = 27395.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.060334 restraints weight = 20814.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.060862 restraints weight = 17476.046| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13249 Z= 0.201 Angle : 0.602 11.123 18505 Z= 0.328 Chirality : 0.039 0.205 2128 Planarity : 0.004 0.075 1842 Dihedral : 15.894 90.211 2939 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.29 % Allowed : 12.88 % Favored : 83.83 % 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: 0.84 (0.24), residues: 1178 helix: 1.45 (0.21), residues: 597 sheet: 0.10 (0.59), residues: 76 loop : -0.39 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1333 TYR 0.026 0.002 TYR B1265 PHE 0.013 0.002 PHE B 462 TRP 0.015 0.001 TRP B 464 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.20 (13249) covalent geometry : angle 0.60242 / 0.33 (18505) hydrogen bonds : bond 0.04712 / 2.75 ( 590) hydrogen bonds : angle 5.01494 / 2.81 ( 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 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8939 (tptt) REVERT: B 80 CYS cc_start: 0.8287 (m) cc_final: 0.8011 (m) REVERT: B 682 PHE cc_start: 0.8604 (m-80) cc_final: 0.8296 (m-80) REVERT: B 933 GLN cc_start: 0.9541 (tp-100) cc_final: 0.9177 (tp-100) REVERT: B 1043 MET cc_start: 0.6057 (ttp) cc_final: 0.5507 (tmm) REVERT: B 1089 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8500 (mtt) REVERT: B 1170 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8586 (mt-10) REVERT: B 1357 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8691 (mp0) outliers start: 35 outliers final: 22 residues processed: 114 average time/residue: 0.1174 time to fit residues: 19.6793 Evaluate side-chains 107 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 218 LYS 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 724 ILE 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 1089 MET 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 1266 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 0.0370 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 HIS B1261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.070726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.056230 restraints weight = 78368.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.057928 restraints weight = 42137.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.059064 restraints weight = 27826.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.059801 restraints weight = 21060.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.060196 restraints weight = 17631.793| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13249 Z= 0.193 Angle : 0.585 10.325 18505 Z= 0.318 Chirality : 0.039 0.198 2128 Planarity : 0.004 0.072 1842 Dihedral : 15.856 89.956 2937 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.76 % Allowed : 12.50 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1178 helix: 1.49 (0.21), residues: 596 sheet: 0.06 (0.58), residues: 76 loop : -0.41 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 976 TYR 0.019 0.002 TYR B1265 PHE 0.012 0.002 PHE B 238 TRP 0.025 0.002 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (13249) covalent geometry : angle 0.58535 / 0.32 (18505) hydrogen bonds : bond 0.04676 / 2.73 ( 590) hydrogen bonds : angle 4.89224 / 2.73 ( 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 132 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.429 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: 0.9184 (mmtt) cc_final: 0.8944 (tptt) REVERT: B 80 CYS cc_start: 0.8306 (m) cc_final: 0.8028 (m) REVERT: B 100 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8338 (mtp180) REVERT: B 483 ASP cc_start: 0.8043 (t0) cc_final: 0.7805 (t0) REVERT: B 569 PHE cc_start: 0.9432 (m-80) cc_final: 0.9004 (m-80) REVERT: B 755 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8269 (ptmm) REVERT: B 933 GLN cc_start: 0.9548 (OUTLIER) cc_final: 0.9178 (tp-100) REVERT: B 1043 MET cc_start: 0.5885 (ttp) cc_final: 0.5416 (tmm) REVERT: B 1253 GLU cc_start: 0.9478 (tp30) cc_final: 0.8945 (mm-30) REVERT: B 1357 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8720 (mp0) outliers start: 40 outliers final: 26 residues processed: 117 average time/residue: 0.1195 time to fit residues: 20.5925 Evaluate side-chains 113 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 275 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 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 759 ILE 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 1089 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 129 optimal weight: 30.0000 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 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** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.070220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.055770 restraints weight = 78734.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057450 restraints weight = 41741.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.058472 restraints weight = 27504.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.059232 restraints weight = 21069.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.059720 restraints weight = 17618.193| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13249 Z= 0.207 Angle : 0.602 12.960 18505 Z= 0.324 Chirality : 0.038 0.181 2128 Planarity : 0.004 0.064 1842 Dihedral : 15.894 90.777 2935 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.85 % Allowed : 14.10 % 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: 0.76 (0.24), residues: 1178 helix: 1.37 (0.21), residues: 598 sheet: -0.04 (0.56), residues: 76 loop : -0.41 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 629 TYR 0.023 0.002 TYR B1265 PHE 0.013 0.002 PHE B 462 TRP 0.017 0.002 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 (13249) covalent geometry : angle 0.60179 / 0.32 (18505) hydrogen bonds : bond 0.04750 / 2.76 ( 590) hydrogen bonds : angle 4.90401 / 2.71 ( 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 128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.430 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: 0.9182 (mmtt) cc_final: 0.8950 (tptt) REVERT: B 80 CYS cc_start: 0.8338 (m) cc_final: 0.8053 (m) REVERT: B 100 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.7905 (mtm-85) REVERT: B 483 ASP cc_start: 0.8026 (t0) cc_final: 0.7800 (t0) REVERT: B 569 PHE cc_start: 0.9425 (m-80) cc_final: 0.9004 (m-80) REVERT: B 723 HIS cc_start: 0.9529 (t70) cc_final: 0.9034 (m170) REVERT: B 755 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8287 (ptmm) REVERT: B 933 GLN cc_start: 0.9553 (tp-100) cc_final: 0.9077 (tp-100) REVERT: B 1043 MET cc_start: 0.5746 (ttp) cc_final: 0.5359 (tmm) outliers start: 41 outliers final: 26 residues processed: 114 average time/residue: 0.1090 time to fit residues: 18.7498 Evaluate side-chains 109 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1089 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.070761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.056279 restraints weight = 77004.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.057966 restraints weight = 40768.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.059102 restraints weight = 26874.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.059796 restraints weight = 20265.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.060319 restraints weight = 16966.994| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13249 Z= 0.164 Angle : 0.578 11.614 18505 Z= 0.310 Chirality : 0.039 0.233 2128 Planarity : 0.004 0.054 1842 Dihedral : 15.878 91.436 2935 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.91 % Allowed : 14.94 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1178 helix: 1.41 (0.21), residues: 599 sheet: -0.01 (0.57), residues: 78 loop : -0.29 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 629 TYR 0.018 0.001 TYR B1265 PHE 0.021 0.001 PHE B1235 TRP 0.014 0.001 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (13249) covalent geometry : angle 0.57795 / 0.31 (18505) hydrogen bonds : bond 0.04349 / 2.52 ( 590) hydrogen bonds : angle 4.74887 / 2.62 ( 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 118 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8931 (tptt) REVERT: B 80 CYS cc_start: 0.8292 (m) cc_final: 0.8000 (m) REVERT: B 100 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.7844 (mtm-85) REVERT: B 161 MET cc_start: 0.8059 (ptt) cc_final: 0.7837 (ptp) REVERT: B 483 ASP cc_start: 0.7983 (t0) cc_final: 0.7745 (t0) REVERT: B 495 MET cc_start: 0.7179 (mtt) cc_final: 0.6887 (mtp) REVERT: B 534 MET cc_start: 0.4278 (ptt) cc_final: 0.3879 (ptt) REVERT: B 569 PHE cc_start: 0.9408 (m-80) cc_final: 0.9020 (m-80) REVERT: B 755 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8417 (ptmm) REVERT: B 1043 MET cc_start: 0.5707 (ttp) cc_final: 0.5322 (tmm) outliers start: 31 outliers final: 25 residues processed: 108 average time/residue: 0.1110 time to fit residues: 18.1157 Evaluate side-chains 104 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 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 1089 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 130 optimal weight: 40.0000 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 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** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.070480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056010 restraints weight = 76689.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.057679 restraints weight = 40590.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.058706 restraints weight = 26718.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059481 restraints weight = 20511.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.059902 restraints weight = 17013.712| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13249 Z= 0.174 Angle : 0.587 12.020 18505 Z= 0.313 Chirality : 0.038 0.194 2128 Planarity : 0.004 0.053 1842 Dihedral : 15.867 90.782 2935 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.91 % Allowed : 15.98 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1178 helix: 1.41 (0.21), residues: 599 sheet: -0.14 (0.56), residues: 78 loop : -0.28 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 629 TYR 0.026 0.002 TYR B 271 PHE 0.014 0.001 PHE B 518 TRP 0.012 0.001 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (13249) covalent geometry : angle 0.58707 / 0.31 (18505) hydrogen bonds : bond 0.04469 / 2.58 ( 590) hydrogen bonds : angle 4.72511 / 2.63 ( 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 108 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.459 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: 0.9192 (mmtt) cc_final: 0.8942 (tptt) REVERT: B 80 CYS cc_start: 0.8284 (m) cc_final: 0.8003 (m) REVERT: B 100 ARG cc_start: 0.8636 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: B 383 MET cc_start: 0.8802 (tpp) cc_final: 0.8444 (tpp) REVERT: B 483 ASP cc_start: 0.7956 (t0) cc_final: 0.7728 (t0) REVERT: B 495 MET cc_start: 0.7183 (mtt) cc_final: 0.6897 (mtp) REVERT: B 569 PHE cc_start: 0.9428 (m-80) cc_final: 0.9034 (m-80) REVERT: B 679 ILE cc_start: 0.9072 (mm) cc_final: 0.8867 (mm) REVERT: B 755 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8357 (ptmm) REVERT: B 933 GLN cc_start: 0.9568 (tp-100) cc_final: 0.9077 (tp-100) REVERT: B 1043 MET cc_start: 0.5662 (ttp) cc_final: 0.5285 (tmm) outliers start: 31 outliers final: 28 residues processed: 98 average time/residue: 0.1075 time to fit residues: 16.2402 Evaluate side-chains 103 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 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 1089 MET Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1142 SER Chi-restraints excluded: chain B residue 1182 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 281 GLN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.066839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.052579 restraints weight = 80042.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.054100 restraints weight = 43499.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.055099 restraints weight = 29199.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.055711 restraints weight = 22497.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.056160 restraints weight = 19050.949| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 13249 Z= 0.375 Angle : 0.814 10.369 18505 Z= 0.432 Chirality : 0.045 0.192 2128 Planarity : 0.006 0.064 1842 Dihedral : 16.361 88.780 2935 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.48 % Allowed : 15.98 % 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: -0.09 (0.24), residues: 1178 helix: 0.59 (0.20), residues: 600 sheet: -0.79 (0.53), residues: 89 loop : -0.62 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 557 TYR 0.029 0.003 TYR B 271 PHE 0.023 0.002 PHE B 462 TRP 0.020 0.003 TRP B 464 HIS 0.010 0.002 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.37 (13249) covalent geometry : angle 0.81396 / 0.43 (18505) hydrogen bonds : bond 0.07091 / 4.12 ( 590) hydrogen bonds : angle 5.41852 / 3.03 ( 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 105 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9260 (mmtt) cc_final: 0.9027 (tptt) REVERT: B 374 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8688 (ptmt) REVERT: B 534 MET cc_start: 0.4286 (ptt) cc_final: 0.3442 (ptt) REVERT: B 569 PHE cc_start: 0.9514 (m-80) cc_final: 0.9125 (m-80) REVERT: B 679 ILE cc_start: 0.9121 (mm) cc_final: 0.8885 (mm) REVERT: B 933 GLN cc_start: 0.9585 (tp-100) cc_final: 0.9129 (tp-100) REVERT: B 1043 MET cc_start: 0.5743 (ttp) cc_final: 0.5348 (tmm) REVERT: B 1089 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8707 (mtt) outliers start: 37 outliers final: 30 residues processed: 93 average time/residue: 0.0943 time to fit residues: 14.0731 Evaluate side-chains 97 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 374 LYS 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 930 HIS 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 1089 MET Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1142 SER Chi-restraints excluded: chain B residue 1166 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 426 GLN B 459 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.070166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.055714 restraints weight = 76182.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.057387 restraints weight = 40228.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.058470 restraints weight = 26443.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.059149 restraints weight = 19990.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.059647 restraints weight = 16777.489| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13249 Z= 0.140 Angle : 0.614 14.300 18505 Z= 0.324 Chirality : 0.039 0.194 2128 Planarity : 0.004 0.053 1842 Dihedral : 16.100 92.692 2935 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.63 % Allowed : 17.11 % 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: 0.61 (0.25), residues: 1178 helix: 1.16 (0.21), residues: 597 sheet: -0.42 (0.54), residues: 88 loop : -0.26 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 629 TYR 0.026 0.002 TYR B 271 PHE 0.017 0.001 PHE B 518 TRP 0.014 0.001 TRP B 464 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (13249) covalent geometry : angle 0.61385 / 0.32 (18505) hydrogen bonds : bond 0.04384 / 2.52 ( 590) hydrogen bonds : angle 4.81941 / 2.65 ( 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 108 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.460 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: 0.9183 (mmtt) cc_final: 0.8916 (tptt) REVERT: B 80 CYS cc_start: 0.8270 (m) cc_final: 0.7976 (m) REVERT: B 100 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8098 (ptp-170) REVERT: B 161 MET cc_start: 0.8216 (ptm) cc_final: 0.7916 (ptm) REVERT: B 419 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9049 (mm) REVERT: B 534 MET cc_start: 0.4025 (ptt) cc_final: 0.3136 (ptt) REVERT: B 569 PHE cc_start: 0.9428 (m-80) cc_final: 0.9056 (m-80) REVERT: B 645 ASP cc_start: 0.9304 (p0) cc_final: 0.9000 (t0) REVERT: B 679 ILE cc_start: 0.9143 (mm) cc_final: 0.8941 (mm) REVERT: B 755 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8094 (ptmm) REVERT: B 1043 MET cc_start: 0.5693 (ttp) cc_final: 0.5338 (tmm) outliers start: 28 outliers final: 22 residues processed: 100 average time/residue: 0.1069 time to fit residues: 16.1917 Evaluate side-chains 94 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 419 LEU 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 1089 MET Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.070045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.055505 restraints weight = 77075.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.057189 restraints weight = 39868.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.058265 restraints weight = 26014.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.058970 restraints weight = 19772.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.059458 restraints weight = 16558.132| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13249 Z= 0.151 Angle : 0.599 12.803 18505 Z= 0.321 Chirality : 0.038 0.171 2128 Planarity : 0.004 0.052 1842 Dihedral : 15.990 87.857 2935 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.16 % Allowed : 17.67 % Favored : 80.17 % 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: 0.72 (0.25), residues: 1178 helix: 1.24 (0.21), residues: 598 sheet: -0.33 (0.57), residues: 80 loop : -0.22 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 307 TYR 0.033 0.002 TYR B 271 PHE 0.015 0.001 PHE B 518 TRP 0.010 0.001 TRP B 464 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (13249) covalent geometry : angle 0.59941 / 0.32 (18505) hydrogen bonds : bond 0.04366 / 2.52 ( 590) hydrogen bonds : angle 4.77805 / 2.65 ( 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 93 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8960 (tptt) REVERT: B 80 CYS cc_start: 0.8334 (m) cc_final: 0.8039 (m) REVERT: B 100 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8131 (ptp-170) REVERT: B 383 MET cc_start: 0.8517 (tpp) cc_final: 0.7890 (tpp) REVERT: B 495 MET cc_start: 0.7227 (mtt) cc_final: 0.6942 (mtp) REVERT: B 534 MET cc_start: 0.4047 (ptt) cc_final: 0.3169 (ptt) REVERT: B 569 PHE cc_start: 0.9453 (m-80) cc_final: 0.9064 (m-80) REVERT: B 645 ASP cc_start: 0.9278 (p0) cc_final: 0.9037 (t0) REVERT: B 679 ILE cc_start: 0.9159 (mm) cc_final: 0.8951 (mm) REVERT: B 755 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8082 (ptmm) REVERT: B 1043 MET cc_start: 0.5686 (ttp) cc_final: 0.5311 (tmm) outliers start: 23 outliers final: 21 residues processed: 85 average time/residue: 0.0967 time to fit residues: 13.0565 Evaluate side-chains 88 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 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 1089 MET Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 103 optimal weight: 0.0270 chunk 14 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.070842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.056419 restraints weight = 76101.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.058177 restraints weight = 39554.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.059256 restraints weight = 25555.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.059980 restraints weight = 19334.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.060408 restraints weight = 16141.523| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13249 Z= 0.124 Angle : 0.580 13.906 18505 Z= 0.307 Chirality : 0.038 0.196 2128 Planarity : 0.003 0.052 1842 Dihedral : 15.855 86.264 2935 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.88 % Allowed : 18.05 % Favored : 80.08 % 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: 0.82 (0.25), residues: 1178 helix: 1.28 (0.21), residues: 605 sheet: -0.38 (0.56), residues: 88 loop : -0.10 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 629 TYR 0.029 0.001 TYR B 271 PHE 0.035 0.001 PHE B 518 TRP 0.006 0.001 TRP B 476 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (13249) covalent geometry : angle 0.57975 / 0.31 (18505) hydrogen bonds : bond 0.03895 / 2.25 ( 590) hydrogen bonds : angle 4.61589 / 2.55 ( 1588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.30 seconds wall clock time: 42 minutes 56.47 seconds (2576.47 seconds total)