Starting phenix.real_space_refine on Thu Aug 6 02:40:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyq_35827/08_2026/8iyq_35827_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyq_35827/08_2026/8iyq_35827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2026/8iyq_35827_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2026/8iyq_35827_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2026/8iyq_35827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2026/8iyq_35827.map" } resolution = 2.46 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= 0.018 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 147 5.49 5 S 19 5.16 5 C 7786 2.51 5 N 2284 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13081 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1198, 9972 Classifications: {'peptide': 1198} Link IDs: {'PTRANS': 30, 'TRANS': 1167} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1198, 9972 Classifications: {'peptide': 1198} Link IDs: {'PTRANS': 30, 'TRANS': 1167} Chain breaks: 2 bond proxies already assigned to first conformer: 10172 Chain: "F" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "O" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2332 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 59, 'rna3p_pyr': 43} Link IDs: {'rna2p': 6, 'rna3p': 102} Chain breaks: 1 Chain: "S" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP A 672 " occ=0.44 ... (14 atoms not shown) pdb=" OD2BASP A 672 " occ=0.56 Time building chain proxies: 4.33, per 1000 atoms: 0.33 Number of scatterers: 13081 At special positions: 0 Unit cell: (100.672, 112.58, 150.468, 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 147 15.00 O 2845 8.00 N 2284 7.00 C 7786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 718.8 milliseconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 16 sheets defined 45.2% alpha, 12.1% beta 62 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 removed outlier: 4.246A pdb=" N GLY A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 89 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.707A pdb=" N HIS A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 317 through 334 removed outlier: 4.247A pdb=" N TYR A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 6.249A pdb=" N GLU A 338 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 452 through 465 removed outlier: 3.526A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.677A pdb=" N PHE A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.592A pdb=" N THR A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 576 through 588 Proline residue: A 585 - end of helix Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.585A pdb=" N ARG A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.990A pdb=" N LEU A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 932 through 943 removed outlier: 4.251A pdb=" N LYS A 936 " --> pdb=" O ARG A 932 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 976 Processing helix chain 'A' and resid 977 through 998 Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1032 through 1044 Processing helix chain 'A' and resid 1045 through 1054 Processing helix chain 'A' and resid 1059 through 1070 removed outlier: 3.900A pdb=" N ARG A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A1065 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU A1066 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1111 Processing helix chain 'A' and resid 1193 through 1198 Processing helix chain 'A' and resid 1202 through 1216 Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1225 through 1235 Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1265 through 1270 removed outlier: 3.818A pdb=" N LYS A1269 " --> pdb=" O GLY A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1309 Processing helix chain 'A' and resid 1353 through 1358 Processing helix chain 'A' and resid 1410 through 1415 removed outlier: 4.159A pdb=" N THR A1414 " --> pdb=" O ARG A1410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 removed outlier: 6.534A pdb=" N LYS A 21 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A 31 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 23 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY A 29 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.754A pdb=" N LYS A 107 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 205 Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 215 removed outlier: 4.339A pdb=" N GLU A 214 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 400 removed outlier: 5.338A pdb=" N LEU A 412 " --> pdb=" O CYS A 393 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU A 395 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N GLN A 410 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N PHE A 397 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N HIS A 408 " --> pdb=" O PHE A 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AA9, first strand: chain 'A' and resid 1003 through 1006 Processing sheet with id=AB1, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 4.016A pdb=" N GLN A1094 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1124 through 1126 Processing sheet with id=AB3, first strand: chain 'A' and resid 1130 through 1137 Processing sheet with id=AB4, first strand: chain 'A' and resid 1166 through 1168 removed outlier: 4.349A pdb=" N LEU A1181 " --> pdb=" O VAL A1168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1260 through 1261 Processing sheet with id=AB6, first strand: chain 'A' and resid 1293 through 1297 removed outlier: 6.065A pdb=" N PHE A1283 " --> pdb=" O ASP A1327 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A1327 " --> pdb=" O PHE A1283 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1285 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1370 through 1375 removed outlier: 6.924A pdb=" N GLU A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR A1366 " --> pdb=" O GLU A1370 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR A1372 " --> pdb=" O GLU A1364 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A1333 " --> pdb=" O ILE A1418 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 152 hydrogen bonds 292 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1898 1.31 - 1.44: 4460 1.44 - 1.56: 6978 1.56 - 1.68: 291 1.68 - 1.81: 31 Bond restraints: 13658 Sorted by residual: bond pdb=" C VAL A 622 " pdb=" O VAL A 622 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.11e-02 8.12e+03 1.89e+01 bond pdb=" CA THR A 502 " pdb=" C THR A 502 " ideal model delta sigma weight residual 1.524 1.487 0.038 1.24e-02 6.50e+03 9.17e+00 bond pdb=" N LYS A1058 " pdb=" CA LYS A1058 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 6.99e+00 bond pdb=" CA VAL A 622 " pdb=" C VAL A 622 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.18e-02 7.18e+03 6.57e+00 bond pdb=" C3' DC F 36 " pdb=" C2' DC F 36 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.49e+00 ... (remaining 13653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 18558 1.75 - 3.50: 494 3.50 - 5.24: 26 5.24 - 6.99: 7 6.99 - 8.74: 1 Bond angle restraints: 19086 Sorted by residual: angle pdb=" C VAL A 622 " pdb=" CA VAL A 622 " pdb=" CB VAL A 622 " ideal model delta sigma weight residual 111.81 105.81 6.00 1.25e+00 6.40e-01 2.31e+01 angle pdb=" O4' DC F 53 " pdb=" C4' DC F 53 " pdb=" C3' DC F 53 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" C4' G O 89 " pdb=" C3' G O 89 " pdb=" O3' G O 89 " ideal model delta sigma weight residual 113.00 104.26 8.74 2.00e+00 2.50e-01 1.91e+01 angle pdb=" N ILE A1343 " pdb=" CA ILE A1343 " pdb=" C ILE A1343 " ideal model delta sigma weight residual 106.55 112.86 -6.31 1.45e+00 4.76e-01 1.89e+01 angle pdb=" O3' G O 89 " pdb=" C3' G O 89 " pdb=" C2' G O 89 " ideal model delta sigma weight residual 113.70 120.22 -6.52 1.60e+00 3.91e-01 1.66e+01 ... (remaining 19081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 7427 23.78 - 47.55: 563 47.55 - 71.33: 221 71.33 - 95.11: 36 95.11 - 118.88: 2 Dihedral angle restraints: 8249 sinusoidal: 4722 harmonic: 3527 Sorted by residual: dihedral pdb=" C4' G O 107 " pdb=" C3' G O 107 " pdb=" O3' G O 107 " pdb=" P C O 108 " ideal model delta sinusoidal sigma weight residual 220.00 101.62 118.38 1 3.50e+01 8.16e-04 1.16e+01 dihedral pdb=" CA ASP A 517 " pdb=" CB ASP A 517 " pdb=" CG ASP A 517 " pdb=" OD1 ASP A 517 " ideal model delta sinusoidal sigma weight residual -30.00 -86.89 56.89 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU A1255 " pdb=" CG GLU A1255 " pdb=" CD GLU A1255 " pdb=" OE1 GLU A1255 " ideal model delta sinusoidal sigma weight residual 0.00 86.77 -86.77 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1467 0.034 - 0.067: 397 0.067 - 0.101: 159 0.101 - 0.134: 113 0.134 - 0.168: 22 Chirality restraints: 2158 Sorted by residual: chirality pdb=" C3' DC F 53 " pdb=" C4' DC F 53 " pdb=" O3' DC F 53 " pdb=" C2' DC F 53 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" C3' DG F 47 " pdb=" C4' DG F 47 " pdb=" O3' DG F 47 " pdb=" C2' DG F 47 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" C3' DC F 49 " pdb=" C4' DC F 49 " pdb=" O3' DC F 49 " pdb=" C2' DC F 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 2155 not shown) Planarity restraints: 1901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 645 " -0.025 2.00e-02 2.50e+03 1.77e-02 6.26e+00 pdb=" CG TYR A 645 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 645 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 645 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 645 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 645 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 645 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 645 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 479 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LYS A 479 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 479 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 480 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 36 " -0.020 2.00e-02 2.50e+03 1.17e-02 3.06e+00 pdb=" N1 C O 36 " 0.027 2.00e-02 2.50e+03 pdb=" C2 C O 36 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C O 36 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C O 36 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C O 36 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C O 36 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C O 36 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C O 36 " 0.004 2.00e-02 2.50e+03 ... (remaining 1898 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3867 2.82 - 3.34: 12264 3.34 - 3.86: 23581 3.86 - 4.38: 28162 4.38 - 4.90: 43444 Nonbonded interactions: 111318 Sorted by model distance: nonbonded pdb=" OG1 THR A1163 " pdb=" OP2 DC F 36 " model vdw 2.305 3.040 nonbonded pdb=" O2' G O 107 " pdb=" OP1 C O 108 " model vdw 2.312 3.040 nonbonded pdb=" O PRO A1244 " pdb=" O2' U O 30 " model vdw 2.313 3.040 nonbonded pdb=" O VAL A 243 " pdb=" OD1 ASP A 244 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN A1129 " pdb=" O2' C O 87 " model vdw 2.331 3.040 ... (remaining 111313 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.450 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 17.020 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:9.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13658 Z= 0.247 Angle : 0.587 8.741 19086 Z= 0.440 Chirality : 0.045 0.168 2158 Planarity : 0.003 0.043 1901 Dihedral : 18.287 118.883 5967 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.54 % Allowed : 1.09 % Favored : 98.37 % 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: 0.39 (0.25), residues: 1195 helix: 1.79 (0.25), residues: 465 sheet: -0.90 (0.43), residues: 130 loop : -0.69 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1145 TYR 0.041 0.001 TYR A 645 PHE 0.017 0.001 PHE A 425 TRP 0.010 0.001 TRP A 487 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.25 (13658) covalent geometry : angle 0.58661 / 0.44 (19086) hydrogen bonds : bond 0.13160 / 8.98 ( 564) hydrogen bonds : angle 5.30537 / 3.73 ( 1438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 233 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8309 (m) cc_final: 0.7710 (t) REVERT: A 41 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6381 (ttp) REVERT: A 63 LYS cc_start: 0.7480 (ttpp) cc_final: 0.7150 (ttpp) REVERT: A 102 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 138 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6481 (mp0) REVERT: A 188 LEU cc_start: 0.7854 (tp) cc_final: 0.7616 (tp) REVERT: A 272 LYS cc_start: 0.7280 (ttmm) cc_final: 0.7019 (ttmm) REVERT: A 290 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7525 (mtmm) REVERT: A 349 ILE cc_start: 0.7139 (mt) cc_final: 0.6938 (mp) REVERT: A 374 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 432 PHE cc_start: 0.7300 (m-10) cc_final: 0.7086 (m-10) REVERT: A 449 PHE cc_start: 0.8000 (m-10) cc_final: 0.7670 (m-10) REVERT: A 461 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6666 (tp30) REVERT: A 468 GLU cc_start: 0.7469 (tt0) cc_final: 0.7264 (tt0) REVERT: A 472 LYS cc_start: 0.7349 (tppt) cc_final: 0.7105 (tppt) REVERT: A 491 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 518 PHE cc_start: 0.7996 (t80) cc_final: 0.7697 (t80) REVERT: A 535 ASN cc_start: 0.7745 (p0) cc_final: 0.7454 (p0) REVERT: A 554 ASP cc_start: 0.7574 (t0) cc_final: 0.7255 (p0) REVERT: A 559 PHE cc_start: 0.7501 (t80) cc_final: 0.7248 (t80) REVERT: A 571 GLU cc_start: 0.7853 (pt0) cc_final: 0.7601 (pt0) REVERT: A 608 LYS cc_start: 0.5916 (mttp) cc_final: 0.5555 (tmtt) REVERT: A 706 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7903 (tttt) REVERT: A 707 ASP cc_start: 0.7878 (t70) cc_final: 0.7611 (t0) REVERT: A 954 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 971 GLN cc_start: 0.6914 (tp-100) cc_final: 0.6517 (tp40) REVERT: A 1107 LYS cc_start: 0.7213 (tttp) cc_final: 0.7004 (ttmt) REVERT: A 1132 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 1144 GLU cc_start: 0.7746 (pt0) cc_final: 0.7529 (pt0) REVERT: A 1145 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7206 (mtp85) REVERT: A 1159 MET cc_start: 0.8665 (mtm) cc_final: 0.8404 (mtp) REVERT: A 1177 LYS cc_start: 0.8241 (tmtt) cc_final: 0.7940 (tmtt) REVERT: A 1221 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 1227 GLU cc_start: 0.7263 (mp0) cc_final: 0.6963 (mp0) REVERT: A 1237 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7264 (tp30) REVERT: A 1269 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7818 (mtmp) REVERT: A 1290 LYS cc_start: 0.7071 (mmpt) cc_final: 0.6832 (mmpt) REVERT: A 1319 GLU cc_start: 0.7068 (mp0) cc_final: 0.6639 (mp0) REVERT: A 1388 LYS cc_start: 0.7224 (mtpp) cc_final: 0.7001 (mtpp) REVERT: A 1425 ASN cc_start: 0.7406 (m110) cc_final: 0.6933 (m-40) outliers start: 6 outliers final: 2 residues processed: 237 average time/residue: 0.6697 time to fit residues: 169.9807 Evaluate side-chains 210 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 932 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 283 GLN A 454 GLN A 458 ASN A 594 ASN ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.140930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113762 restraints weight = 36143.639| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.39 r_work: 0.3350 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13658 Z= 0.181 Angle : 0.562 7.924 19086 Z= 0.323 Chirality : 0.042 0.277 2158 Planarity : 0.004 0.045 1901 Dihedral : 18.882 118.660 3380 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.09 % Allowed : 9.62 % Favored : 89.29 % 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: 0.24 (0.25), residues: 1195 helix: 1.45 (0.24), residues: 475 sheet: -0.92 (0.42), residues: 140 loop : -0.62 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1410 TYR 0.036 0.002 TYR A 645 PHE 0.025 0.002 PHE A 425 TRP 0.018 0.002 TRP A 487 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (13658) covalent geometry : angle 0.56238 / 0.32 (19086) hydrogen bonds : bond 0.05342 / 3.62 ( 564) hydrogen bonds : angle 4.04042 / 2.87 ( 1438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8799 (m) cc_final: 0.8544 (t) REVERT: A 41 MET cc_start: 0.7452 (ttp) cc_final: 0.7202 (ttp) REVERT: A 486 ARG cc_start: 0.7824 (ptm-80) cc_final: 0.7590 (ptm-80) REVERT: A 683 VAL cc_start: 0.8306 (m) cc_final: 0.8105 (t) REVERT: A 707 ASP cc_start: 0.7857 (t70) cc_final: 0.7607 (t0) REVERT: A 938 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 941 ILE cc_start: 0.8625 (mm) cc_final: 0.8361 (tp) REVERT: A 970 THR cc_start: 0.8007 (t) cc_final: 0.7748 (p) REVERT: A 971 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7117 (tp40) REVERT: A 975 ASP cc_start: 0.7348 (m-30) cc_final: 0.6629 (m-30) REVERT: A 1000 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8097 (mmmt) REVERT: A 1159 MET cc_start: 0.8746 (mtm) cc_final: 0.8509 (mtp) REVERT: A 1322 SER cc_start: 0.8333 (m) cc_final: 0.8114 (p) REVERT: A 1425 ASN cc_start: 0.8308 (m110) cc_final: 0.8012 (m-40) outliers start: 12 outliers final: 8 residues processed: 221 average time/residue: 0.6508 time to fit residues: 154.0757 Evaluate side-chains 215 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1339 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 458 ASN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A 998 ASN ** A1009 HIS ** 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 = 0.3867 r_free = 0.3867 target = 0.138993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111292 restraints weight = 38257.901| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.72 r_work: 0.3332 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13658 Z= 0.194 Angle : 0.562 6.983 19086 Z= 0.323 Chirality : 0.042 0.273 2158 Planarity : 0.004 0.045 1901 Dihedral : 18.814 120.134 3377 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.81 % Allowed : 12.34 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1195 helix: 1.30 (0.24), residues: 475 sheet: -0.84 (0.43), residues: 134 loop : -0.70 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1410 TYR 0.036 0.002 TYR A 645 PHE 0.024 0.002 PHE A 425 TRP 0.024 0.002 TRP A 487 HIS 0.018 0.002 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (13658) covalent geometry : angle 0.56227 / 0.32 (19086) hydrogen bonds : bond 0.05274 / 3.55 ( 564) hydrogen bonds : angle 3.96054 / 2.81 ( 1438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 12 THR cc_start: 0.8811 (m) cc_final: 0.8570 (t) REVERT: A 41 MET cc_start: 0.7531 (ttp) cc_final: 0.7235 (ttp) REVERT: A 272 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7651 (ttmm) REVERT: A 485 HIS cc_start: 0.7872 (m-70) cc_final: 0.7662 (m-70) REVERT: A 535 ASN cc_start: 0.7963 (p0) cc_final: 0.7742 (p0) REVERT: A 683 VAL cc_start: 0.8360 (m) cc_final: 0.8137 (t) REVERT: A 707 ASP cc_start: 0.7889 (t70) cc_final: 0.7618 (t0) REVERT: A 970 THR cc_start: 0.8003 (t) cc_final: 0.7664 (m) REVERT: A 971 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7428 (tp40) REVERT: A 1000 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8145 (mmmt) REVERT: A 1005 TRP cc_start: 0.8433 (t-100) cc_final: 0.8126 (t-100) REVERT: A 1425 ASN cc_start: 0.8318 (m110) cc_final: 0.8026 (m-40) outliers start: 20 outliers final: 13 residues processed: 218 average time/residue: 0.7074 time to fit residues: 165.1188 Evaluate side-chains 220 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1195 LYS Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A1009 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.139378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111864 restraints weight = 40563.112| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.77 r_work: 0.3332 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13658 Z= 0.172 Angle : 0.534 6.513 19086 Z= 0.309 Chirality : 0.041 0.279 2158 Planarity : 0.004 0.046 1901 Dihedral : 18.798 121.680 3377 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.91 % Allowed : 12.61 % Favored : 85.48 % 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: 0.10 (0.24), residues: 1195 helix: 1.23 (0.23), residues: 479 sheet: -0.46 (0.45), residues: 124 loop : -0.76 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1410 TYR 0.035 0.002 TYR A 645 PHE 0.023 0.002 PHE A 559 TRP 0.021 0.002 TRP A 641 HIS 0.005 0.001 HIS A 529 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (13658) covalent geometry : angle 0.53370 / 0.31 (19086) hydrogen bonds : bond 0.05032 / 3.37 ( 564) hydrogen bonds : angle 3.90141 / 2.78 ( 1438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8785 (m) cc_final: 0.8544 (t) REVERT: A 41 MET cc_start: 0.7472 (ttp) cc_final: 0.7179 (ttp) REVERT: A 181 HIS cc_start: 0.7898 (m90) cc_final: 0.7520 (m90) REVERT: A 272 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7659 (ttmm) REVERT: A 480 LEU cc_start: 0.8010 (mm) cc_final: 0.7753 (mp) REVERT: A 517 ASP cc_start: 0.6760 (t70) cc_final: 0.6373 (t0) REVERT: A 535 ASN cc_start: 0.7986 (p0) cc_final: 0.7688 (p0) REVERT: A 550 LYS cc_start: 0.8369 (mttt) cc_final: 0.8163 (mttt) REVERT: A 707 ASP cc_start: 0.7808 (t70) cc_final: 0.7531 (t0) REVERT: A 970 THR cc_start: 0.8011 (t) cc_final: 0.7690 (m) REVERT: A 975 ASP cc_start: 0.7450 (m-30) cc_final: 0.7198 (m-30) REVERT: A 998 ASN cc_start: 0.8231 (t0) cc_final: 0.7882 (t0) REVERT: A 1005 TRP cc_start: 0.8457 (t-100) cc_final: 0.8146 (t-100) REVERT: A 1290 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7937 (mmpt) REVERT: A 1425 ASN cc_start: 0.8363 (m110) cc_final: 0.8008 (m-40) outliers start: 21 outliers final: 14 residues processed: 219 average time/residue: 0.6654 time to fit residues: 156.4933 Evaluate side-chains 219 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1195 LYS Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 50.0000 chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 458 ASN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.139368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111648 restraints weight = 36857.898| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.84 r_work: 0.3334 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13658 Z= 0.169 Angle : 0.531 6.375 19086 Z= 0.307 Chirality : 0.040 0.280 2158 Planarity : 0.004 0.045 1901 Dihedral : 18.784 122.099 3377 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.63 % Allowed : 14.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1195 helix: 1.17 (0.23), residues: 479 sheet: -0.40 (0.45), residues: 124 loop : -0.74 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1410 TYR 0.032 0.002 TYR A 645 PHE 0.022 0.001 PHE A 425 TRP 0.022 0.002 TRP A 641 HIS 0.007 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (13658) covalent geometry : angle 0.53060 / 0.31 (19086) hydrogen bonds : bond 0.04920 / 3.30 ( 564) hydrogen bonds : angle 3.89256 / 2.78 ( 1438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8775 (m) cc_final: 0.8537 (t) REVERT: A 41 MET cc_start: 0.7590 (ttp) cc_final: 0.7342 (ttp) REVERT: A 181 HIS cc_start: 0.7882 (m90) cc_final: 0.7516 (m90) REVERT: A 272 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7663 (ttmm) REVERT: A 410 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7647 (tp40) REVERT: A 535 ASN cc_start: 0.7984 (p0) cc_final: 0.7695 (p0) REVERT: A 550 LYS cc_start: 0.8305 (mttt) cc_final: 0.8077 (mttt) REVERT: A 707 ASP cc_start: 0.7948 (t70) cc_final: 0.7666 (t0) REVERT: A 970 THR cc_start: 0.8042 (t) cc_final: 0.7741 (m) REVERT: A 975 ASP cc_start: 0.7472 (m-30) cc_final: 0.7238 (m-30) REVERT: A 998 ASN cc_start: 0.8208 (t0) cc_final: 0.7853 (t0) REVERT: A 1005 TRP cc_start: 0.8488 (t-100) cc_final: 0.8186 (t-100) REVERT: A 1290 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7982 (mmpt) REVERT: A 1425 ASN cc_start: 0.8363 (m110) cc_final: 0.8006 (m-40) outliers start: 18 outliers final: 14 residues processed: 218 average time/residue: 0.6708 time to fit residues: 157.3247 Evaluate side-chains 225 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 458 ASN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.139230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111771 restraints weight = 29516.062| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.25 r_work: 0.3368 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13658 Z= 0.170 Angle : 0.527 6.358 19086 Z= 0.305 Chirality : 0.040 0.281 2158 Planarity : 0.004 0.045 1901 Dihedral : 18.779 122.198 3377 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.63 % Allowed : 14.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1195 helix: 1.16 (0.23), residues: 479 sheet: -0.51 (0.44), residues: 130 loop : -0.71 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1410 TYR 0.032 0.002 TYR A 645 PHE 0.021 0.002 PHE A 425 TRP 0.024 0.002 TRP A 641 HIS 0.005 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (13658) covalent geometry : angle 0.52708 / 0.31 (19086) hydrogen bonds : bond 0.04897 / 3.28 ( 564) hydrogen bonds : angle 3.88451 / 2.78 ( 1438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8820 (m) cc_final: 0.8567 (t) REVERT: A 41 MET cc_start: 0.7718 (ttp) cc_final: 0.7449 (ttp) REVERT: A 181 HIS cc_start: 0.7978 (m90) cc_final: 0.7628 (m90) REVERT: A 272 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7723 (ttmm) REVERT: A 410 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7738 (tp40) REVERT: A 535 ASN cc_start: 0.8086 (p0) cc_final: 0.7792 (p0) REVERT: A 550 LYS cc_start: 0.8419 (mttt) cc_final: 0.8185 (mttt) REVERT: A 707 ASP cc_start: 0.8225 (t70) cc_final: 0.7958 (t0) REVERT: A 970 THR cc_start: 0.8082 (t) cc_final: 0.7771 (m) REVERT: A 975 ASP cc_start: 0.7548 (m-30) cc_final: 0.7325 (m-30) REVERT: A 998 ASN cc_start: 0.8341 (t0) cc_final: 0.7984 (t0) REVERT: A 1005 TRP cc_start: 0.8510 (t-100) cc_final: 0.8205 (t-100) REVERT: A 1425 ASN cc_start: 0.8518 (m110) cc_final: 0.8166 (m-40) outliers start: 18 outliers final: 17 residues processed: 217 average time/residue: 0.6452 time to fit residues: 150.4913 Evaluate side-chains 227 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1195 LYS Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113938 restraints weight = 34322.664| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.53 r_work: 0.3349 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13658 Z= 0.177 Angle : 0.536 6.762 19086 Z= 0.309 Chirality : 0.041 0.282 2158 Planarity : 0.004 0.045 1901 Dihedral : 18.782 122.072 3377 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.81 % Allowed : 14.70 % Favored : 83.48 % 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: 0.03 (0.24), residues: 1195 helix: 1.14 (0.23), residues: 479 sheet: -0.54 (0.44), residues: 130 loop : -0.75 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1410 TYR 0.031 0.002 TYR A 645 PHE 0.022 0.001 PHE A 425 TRP 0.028 0.002 TRP A 641 HIS 0.013 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (13658) covalent geometry : angle 0.53634 / 0.31 (19086) hydrogen bonds : bond 0.04958 / 3.32 ( 564) hydrogen bonds : angle 3.88302 / 2.77 ( 1438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8745 (m) cc_final: 0.8500 (t) REVERT: A 41 MET cc_start: 0.7550 (ttp) cc_final: 0.7314 (ttp) REVERT: A 181 HIS cc_start: 0.7924 (m90) cc_final: 0.7540 (m90) REVERT: A 272 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7632 (ttmm) REVERT: A 410 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7628 (tp40) REVERT: A 535 ASN cc_start: 0.8020 (p0) cc_final: 0.7741 (p0) REVERT: A 550 LYS cc_start: 0.8314 (mttt) cc_final: 0.8059 (mttt) REVERT: A 970 THR cc_start: 0.8042 (t) cc_final: 0.7722 (m) REVERT: A 975 ASP cc_start: 0.7461 (m-30) cc_final: 0.7253 (m-30) REVERT: A 998 ASN cc_start: 0.8191 (t0) cc_final: 0.7838 (t0) REVERT: A 1005 TRP cc_start: 0.8510 (t-100) cc_final: 0.8219 (t-100) REVERT: A 1071 MET cc_start: 0.7153 (mtp) cc_final: 0.6857 (mtp) REVERT: A 1425 ASN cc_start: 0.8365 (m110) cc_final: 0.7994 (m-40) outliers start: 20 outliers final: 18 residues processed: 220 average time/residue: 0.6635 time to fit residues: 156.7260 Evaluate side-chains 228 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1195 LYS Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 chunk 101 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 477 HIS ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112958 restraints weight = 38134.766| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.82 r_work: 0.3360 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13658 Z= 0.125 Angle : 0.507 9.170 19086 Z= 0.296 Chirality : 0.038 0.275 2158 Planarity : 0.004 0.043 1901 Dihedral : 18.768 124.245 3377 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.27 % Allowed : 15.25 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1195 helix: 1.23 (0.23), residues: 479 sheet: -0.49 (0.44), residues: 130 loop : -0.70 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 549 TYR 0.031 0.001 TYR A 645 PHE 0.020 0.001 PHE A 425 TRP 0.032 0.001 TRP A 641 HIS 0.005 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (13658) covalent geometry : angle 0.50733 / 0.30 (19086) hydrogen bonds : bond 0.04409 / 2.96 ( 564) hydrogen bonds : angle 3.83140 / 2.74 ( 1438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8747 (m) cc_final: 0.8498 (t) REVERT: A 41 MET cc_start: 0.7584 (ttp) cc_final: 0.7338 (ttp) REVERT: A 181 HIS cc_start: 0.7837 (m90) cc_final: 0.7488 (m90) REVERT: A 272 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7630 (ttmm) REVERT: A 410 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7660 (tp-100) REVERT: A 535 ASN cc_start: 0.7992 (p0) cc_final: 0.7726 (p0) REVERT: A 550 LYS cc_start: 0.8345 (mttt) cc_final: 0.8085 (mttt) REVERT: A 597 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7140 (mp0) REVERT: A 941 ILE cc_start: 0.8591 (mm) cc_final: 0.8376 (tp) REVERT: A 970 THR cc_start: 0.7996 (t) cc_final: 0.7705 (m) REVERT: A 998 ASN cc_start: 0.8194 (t0) cc_final: 0.7840 (t0) REVERT: A 1005 TRP cc_start: 0.8491 (t-100) cc_final: 0.8207 (t-100) REVERT: A 1071 MET cc_start: 0.7095 (mtp) cc_final: 0.6794 (mtp) REVERT: A 1425 ASN cc_start: 0.8366 (m110) cc_final: 0.7995 (m-40) outliers start: 14 outliers final: 13 residues processed: 219 average time/residue: 0.6724 time to fit residues: 158.1918 Evaluate side-chains 222 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 10 optimal weight: 0.0470 chunk 129 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 458 ASN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114890 restraints weight = 44995.113| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.80 r_work: 0.3334 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13658 Z= 0.151 Angle : 0.527 9.127 19086 Z= 0.304 Chirality : 0.039 0.279 2158 Planarity : 0.004 0.044 1901 Dihedral : 18.754 123.426 3377 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.54 % Allowed : 15.61 % Favored : 82.85 % 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: 1195 helix: 1.15 (0.23), residues: 479 sheet: -0.43 (0.45), residues: 130 loop : -0.71 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1410 TYR 0.030 0.001 TYR A 645 PHE 0.021 0.001 PHE A 425 TRP 0.038 0.002 TRP A 641 HIS 0.009 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13658) covalent geometry : angle 0.52711 / 0.30 (19086) hydrogen bonds : bond 0.04571 / 3.07 ( 564) hydrogen bonds : angle 3.84563 / 2.75 ( 1438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8758 (m) cc_final: 0.8500 (t) REVERT: A 41 MET cc_start: 0.7544 (ttp) cc_final: 0.7292 (ttp) REVERT: A 181 HIS cc_start: 0.7992 (m90) cc_final: 0.7644 (m90) REVERT: A 272 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7644 (ttmm) REVERT: A 410 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7639 (tp-100) REVERT: A 461 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: A 535 ASN cc_start: 0.7999 (p0) cc_final: 0.7745 (p0) REVERT: A 550 LYS cc_start: 0.8335 (mttt) cc_final: 0.8077 (mttt) REVERT: A 597 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7192 (mp0) REVERT: A 970 THR cc_start: 0.8025 (t) cc_final: 0.7723 (m) REVERT: A 998 ASN cc_start: 0.8208 (t0) cc_final: 0.7871 (t0) REVERT: A 1005 TRP cc_start: 0.8504 (t-100) cc_final: 0.8275 (t-100) REVERT: A 1071 MET cc_start: 0.7128 (mtp) cc_final: 0.6820 (mtp) REVERT: A 1425 ASN cc_start: 0.8379 (m110) cc_final: 0.8001 (m-40) outliers start: 17 outliers final: 15 residues processed: 219 average time/residue: 0.6826 time to fit residues: 160.5846 Evaluate side-chains 227 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.0050 chunk 113 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 130 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 458 ASN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116898 restraints weight = 23516.398| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.89 r_work: 0.3420 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13658 Z= 0.127 Angle : 0.515 9.764 19086 Z= 0.298 Chirality : 0.038 0.276 2158 Planarity : 0.004 0.044 1901 Dihedral : 18.752 123.999 3377 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.36 % Allowed : 15.97 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1195 helix: 1.19 (0.24), residues: 479 sheet: -0.41 (0.45), residues: 130 loop : -0.70 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1410 TYR 0.030 0.001 TYR A 645 PHE 0.024 0.001 PHE A 669 TRP 0.044 0.002 TRP A 641 HIS 0.009 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (13658) covalent geometry : angle 0.51450 / 0.30 (19086) hydrogen bonds : bond 0.04365 / 2.93 ( 564) hydrogen bonds : angle 3.81857 / 2.73 ( 1438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8776 (m) cc_final: 0.8509 (t) REVERT: A 41 MET cc_start: 0.7731 (ttp) cc_final: 0.7450 (ttp) REVERT: A 181 HIS cc_start: 0.8010 (m90) cc_final: 0.7657 (m90) REVERT: A 272 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7773 (ttmm) REVERT: A 410 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7697 (tp-100) REVERT: A 461 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 535 ASN cc_start: 0.8042 (p0) cc_final: 0.7783 (p0) REVERT: A 550 LYS cc_start: 0.8399 (mttt) cc_final: 0.8141 (mttt) REVERT: A 597 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7423 (mp0) REVERT: A 970 THR cc_start: 0.8016 (t) cc_final: 0.7714 (m) REVERT: A 998 ASN cc_start: 0.8312 (t0) cc_final: 0.7967 (t0) REVERT: A 1005 TRP cc_start: 0.8519 (t-100) cc_final: 0.8232 (t-100) REVERT: A 1071 MET cc_start: 0.7241 (mtp) cc_final: 0.6939 (mtp) REVERT: A 1425 ASN cc_start: 0.8465 (m110) cc_final: 0.8108 (m-40) outliers start: 15 outliers final: 14 residues processed: 220 average time/residue: 0.6523 time to fit residues: 154.2150 Evaluate side-chains 226 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115625 restraints weight = 40068.413| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.78 r_work: 0.3341 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 13658 Z= 0.173 Angle : 0.796 59.200 19086 Z= 0.495 Chirality : 0.060 2.102 2158 Planarity : 0.004 0.044 1901 Dihedral : 18.751 123.962 3377 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.54 % Allowed : 15.88 % Favored : 82.58 % Cbeta Deviations : 0.09 % 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: 0.12 (0.24), residues: 1195 helix: 1.18 (0.24), residues: 479 sheet: -0.41 (0.45), residues: 130 loop : -0.70 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1410 TYR 0.029 0.001 TYR A 645 PHE 0.019 0.001 PHE A 425 TRP 0.041 0.002 TRP A 641 HIS 0.009 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (13658) covalent geometry : angle 0.79600 / 0.49 (19086) hydrogen bonds : bond 0.04405 / 2.96 ( 564) hydrogen bonds : angle 3.82084 / 2.73 ( 1438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5429.19 seconds wall clock time: 93 minutes 0.22 seconds (5580.22 seconds total)