Starting phenix.real_space_refine on Thu Sep 18 00:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cok_45782/09_2025/9cok_45782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cok_45782/09_2025/9cok_45782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cok_45782/09_2025/9cok_45782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cok_45782/09_2025/9cok_45782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cok_45782/09_2025/9cok_45782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cok_45782/09_2025/9cok_45782.map" } resolution = 2.92 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= 0.067 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 7765 2.51 5 N 2088 2.21 5 O 2273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12206 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 370 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 380 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 452 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 9976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1241, 9976 Classifications: {'peptide': 1241} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 46, 'TRANS': 1194} Chain breaks: 8 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 319 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "F" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 136 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 573 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Time building chain proxies: 3.37, per 1000 atoms: 0.28 Number of scatterers: 12206 At special positions: 0 Unit cell: (104.361, 111.642, 158.564, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2273 8.00 N 2088 7.00 C 7765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 610.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2916 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 7 sheets defined 60.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 542 through 573 Processing helix chain 'D' and resid 533 through 541 Processing helix chain 'D' and resid 542 through 574 removed outlier: 3.750A pdb=" N MET D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 Processing helix chain 'C' and resid 542 through 578 Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.778A pdb=" N LEU A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 87 through 96 removed outlier: 4.909A pdb=" N ASN A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 removed outlier: 3.545A pdb=" N ASP A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.789A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.611A pdb=" N LYS A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 4.177A pdb=" N SER A 194 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.803A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.649A pdb=" N VAL A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 removed outlier: 4.012A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 309 through 326 removed outlier: 3.897A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 362 removed outlier: 4.279A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.854A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 406 Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.597A pdb=" N SER A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 486 removed outlier: 5.653A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 505 through 511 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.701A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.793A pdb=" N TYR A 578 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 579 " --> pdb=" O VAL A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 579' Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.553A pdb=" N ASN A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.236A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.715A pdb=" N LYS A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 912 removed outlier: 3.906A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 972 through 982 Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 4.202A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1083 removed outlier: 3.562A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1110 Processing helix chain 'A' and resid 1115 through 1126 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.613A pdb=" N LEU A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1178 removed outlier: 5.162A pdb=" N ASP A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1209 removed outlier: 5.360A pdb=" N GLU A1206 " --> pdb=" O HIS A1202 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A1207 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1236 through 1241 removed outlier: 3.517A pdb=" N GLU A1240 " --> pdb=" O CYS A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1309 removed outlier: 3.711A pdb=" N GLY A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1323 removed outlier: 3.701A pdb=" N GLU A1317 " --> pdb=" O GLU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1407 Processing helix chain 'E' and resid 538 through 541 removed outlier: 3.685A pdb=" N LYS E 541 " --> pdb=" O GLU E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 541' Processing helix chain 'E' and resid 542 through 573 Processing helix chain 'F' and resid 602 through 607 Processing helix chain 'G' and resid 657 through 672 Processing helix chain 'G' and resid 674 through 686 Processing helix chain 'G' and resid 690 through 704 removed outlier: 3.858A pdb=" N ILE G 694 " --> pdb=" O ASN G 690 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 704 " --> pdb=" O THR G 700 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 385 through 388 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 555 removed outlier: 5.978A pdb=" N TYR A 539 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 825 removed outlier: 3.724A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA6, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AA7, first strand: chain 'A' and resid 1225 through 1230 678 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3994 1.34 - 1.46: 2253 1.46 - 1.58: 6044 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 12423 Sorted by residual: bond pdb=" CB GLU A 881 " pdb=" CG GLU A 881 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CA LYS G 687 " pdb=" CB LYS G 687 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.86e-02 2.89e+03 1.09e+00 bond pdb=" CG LEU G 637 " pdb=" CD1 LEU G 637 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CG LYS A 878 " pdb=" CD LYS A 878 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CB LYS A 878 " pdb=" CG LYS A 878 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.40e-01 ... (remaining 12418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 16548 1.70 - 3.41: 168 3.41 - 5.11: 37 5.11 - 6.81: 8 6.81 - 8.52: 5 Bond angle restraints: 16766 Sorted by residual: angle pdb=" N LEU G 639 " pdb=" CA LEU G 639 " pdb=" C LEU G 639 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.48e+01 angle pdb=" CB LYS A 878 " pdb=" CG LYS A 878 " pdb=" CD LYS A 878 " ideal model delta sigma weight residual 111.30 118.58 -7.28 2.30e+00 1.89e-01 1.00e+01 angle pdb=" N PHE G 652 " pdb=" CA PHE G 652 " pdb=" C PHE G 652 " ideal model delta sigma weight residual 113.21 109.64 3.57 1.15e+00 7.56e-01 9.66e+00 angle pdb=" C ASN A 211 " pdb=" CA ASN A 211 " pdb=" CB ASN A 211 " ideal model delta sigma weight residual 109.56 113.99 -4.43 1.51e+00 4.39e-01 8.61e+00 angle pdb=" C ALA G 649 " pdb=" CA ALA G 649 " pdb=" CB ALA G 649 " ideal model delta sigma weight residual 110.42 116.15 -5.73 1.99e+00 2.53e-01 8.30e+00 ... (remaining 16761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6323 17.73 - 35.46: 935 35.46 - 53.20: 295 53.20 - 70.93: 48 70.93 - 88.66: 24 Dihedral angle restraints: 7625 sinusoidal: 3150 harmonic: 4475 Sorted by residual: dihedral pdb=" CA LEU G 639 " pdb=" C LEU G 639 " pdb=" N PRO G 640 " pdb=" CA PRO G 640 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASN A 405 " pdb=" C ASN A 405 " pdb=" N GLY A 406 " pdb=" CA GLY A 406 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 14 " pdb=" CG GLU A 14 " pdb=" CD GLU A 14 " pdb=" OE1 GLU A 14 " ideal model delta sinusoidal sigma weight residual 0.00 88.66 -88.66 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1358 0.037 - 0.073: 405 0.073 - 0.110: 126 0.110 - 0.147: 27 0.147 - 0.184: 1 Chirality restraints: 1917 Sorted by residual: chirality pdb=" CB ILE A1075 " pdb=" CA ILE A1075 " pdb=" CG1 ILE A1075 " pdb=" CG2 ILE A1075 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA ILE A1445 " pdb=" N ILE A1445 " pdb=" C ILE A1445 " pdb=" CB ILE A1445 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CG LEU G 637 " pdb=" CB LEU G 637 " pdb=" CD1 LEU G 637 " pdb=" CD2 LEU G 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1914 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 639 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.69e+00 pdb=" N PRO G 640 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 640 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 640 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 644 " 0.009 2.00e-02 2.50e+03 1.30e-02 2.97e+00 pdb=" CG PHE G 644 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE G 644 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 644 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE G 644 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 644 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 644 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 643 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C ASN G 643 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN G 643 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE G 644 " 0.010 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1481 2.75 - 3.29: 11869 3.29 - 3.83: 21353 3.83 - 4.36: 24420 4.36 - 4.90: 43057 Nonbonded interactions: 102180 Sorted by model distance: nonbonded pdb=" OD1 ASN B 561 " pdb=" OG1 THR C 560 " model vdw 2.214 3.040 nonbonded pdb=" O LEU A 973 " pdb=" OG SER A 977 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN A1364 " pdb=" OG SER A1367 " model vdw 2.241 3.040 nonbonded pdb=" OG SER A1192 " pdb=" OE1 GLU A1223 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN A 92 " pdb=" OH TYR A 238 " model vdw 2.252 3.040 ... (remaining 102175 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 538 through 578) selection = (chain 'D' and resid 538 through 578) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.210 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: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.100 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.002 0.036 12423 Z= 0.104 Angle : 0.495 8.515 16766 Z= 0.256 Chirality : 0.039 0.184 1917 Planarity : 0.003 0.060 2125 Dihedral : 18.758 88.659 4709 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.66 % Allowed : 33.48 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.23), residues: 1494 helix: 2.66 (0.19), residues: 822 sheet: -0.02 (0.56), residues: 90 loop : -0.19 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 675 TYR 0.011 0.001 TYR A 284 PHE 0.029 0.001 PHE G 644 TRP 0.010 0.001 TRP A1248 HIS 0.004 0.000 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00226 (12423) covalent geometry : angle 0.49490 (16766) hydrogen bonds : bond 0.11033 ( 678) hydrogen bonds : angle 4.86149 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6971 (mm-30) REVERT: D 577 MET cc_start: 0.6477 (tmm) cc_final: 0.6019 (tmm) REVERT: C 559 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8170 (ttmt) REVERT: A 101 GLN cc_start: 0.8525 (mt0) cc_final: 0.8078 (tp40) REVERT: A 152 ARG cc_start: 0.7783 (ttm110) cc_final: 0.7023 (ttp80) REVERT: A 202 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7555 (ttm-80) REVERT: A 261 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7745 (mt) REVERT: A 306 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 339 ASP cc_start: 0.6893 (m-30) cc_final: 0.6548 (m-30) REVERT: A 381 MET cc_start: 0.8696 (mmt) cc_final: 0.8332 (mmt) REVERT: A 419 TYR cc_start: 0.7640 (m-80) cc_final: 0.7301 (m-80) REVERT: A 474 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7287 (mttm) REVERT: A 557 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 799 GLU cc_start: 0.8121 (tt0) cc_final: 0.7503 (pm20) REVERT: A 1011 ASN cc_start: 0.8432 (t0) cc_final: 0.7367 (m110) REVERT: A 1161 ARG cc_start: 0.7696 (mpp80) cc_final: 0.7048 (ttt90) REVERT: A 1186 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6558 (tp) REVERT: A 1310 ASP cc_start: 0.7272 (t0) cc_final: 0.6257 (p0) outliers start: 9 outliers final: 6 residues processed: 196 average time/residue: 0.6948 time to fit residues: 146.2730 Evaluate side-chains 188 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 578 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN A 511 ASN ** A 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127571 restraints weight = 15729.992| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.16 r_work: 0.3392 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12423 Z= 0.113 Angle : 0.475 7.618 16766 Z= 0.247 Chirality : 0.040 0.176 1917 Planarity : 0.004 0.047 2125 Dihedral : 5.218 56.926 1658 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.56 % Allowed : 28.95 % Favored : 65.50 % 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 aren not related in a simple way. whole: 2.05 (0.23), residues: 1494 helix: 2.63 (0.19), residues: 827 sheet: 0.05 (0.53), residues: 95 loop : -0.33 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 675 TYR 0.021 0.001 TYR A1214 PHE 0.021 0.001 PHE G 644 TRP 0.012 0.001 TRP A1248 HIS 0.004 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00256 (12423) covalent geometry : angle 0.47467 (16766) hydrogen bonds : bond 0.03488 ( 678) hydrogen bonds : angle 4.14453 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 182 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6562 (mm-30) REVERT: D 577 MET cc_start: 0.6329 (tmm) cc_final: 0.5856 (tmm) REVERT: C 559 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8027 (ttmt) REVERT: A 44 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7870 (mptt) REVERT: A 101 GLN cc_start: 0.8615 (mt0) cc_final: 0.8152 (tp40) REVERT: A 152 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7215 (ttp-170) REVERT: A 202 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7558 (ttm-80) REVERT: A 261 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 306 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8251 (pp) REVERT: A 331 GLN cc_start: 0.7972 (tm130) cc_final: 0.7403 (tm130) REVERT: A 339 ASP cc_start: 0.7007 (m-30) cc_final: 0.6679 (m-30) REVERT: A 375 GLU cc_start: 0.8316 (tp30) cc_final: 0.8073 (mm-30) REVERT: A 381 MET cc_start: 0.8807 (mmt) cc_final: 0.8437 (mmt) REVERT: A 419 TYR cc_start: 0.7910 (m-80) cc_final: 0.7407 (m-80) REVERT: A 474 LYS cc_start: 0.7593 (mtmm) cc_final: 0.7341 (mttm) REVERT: A 557 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 755 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8648 (ttm) REVERT: A 799 GLU cc_start: 0.8242 (tt0) cc_final: 0.7548 (pm20) REVERT: A 860 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.5930 (tt0) REVERT: A 1011 ASN cc_start: 0.8535 (t0) cc_final: 0.7444 (m110) REVERT: A 1078 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7603 (mpt-90) REVERT: A 1161 ARG cc_start: 0.7844 (mpp80) cc_final: 0.7197 (ttt90) REVERT: A 1186 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6742 (tp) REVERT: E 578 ILE cc_start: 0.6197 (OUTLIER) cc_final: 0.5697 (mp) outliers start: 76 outliers final: 30 residues processed: 234 average time/residue: 0.6453 time to fit residues: 162.9460 Evaluate side-chains 213 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 777 LYS Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 577 MET Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain F residue 604 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN A 858 GLN A 968 ASN ** A1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121825 restraints weight = 15936.903| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.16 r_work: 0.3306 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12423 Z= 0.208 Angle : 0.555 8.379 16766 Z= 0.288 Chirality : 0.044 0.148 1917 Planarity : 0.004 0.052 2125 Dihedral : 5.612 58.818 1654 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.87 % Allowed : 26.54 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: 1.58 (0.22), residues: 1494 helix: 2.26 (0.19), residues: 821 sheet: -0.35 (0.49), residues: 97 loop : -0.48 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.024 0.002 TYR A1214 PHE 0.019 0.002 PHE A 399 TRP 0.011 0.001 TRP A1248 HIS 0.007 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00506 (12423) covalent geometry : angle 0.55465 (16766) hydrogen bonds : bond 0.04377 ( 678) hydrogen bonds : angle 4.28063 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 180 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6660 (mm-30) REVERT: D 577 MET cc_start: 0.6267 (tmm) cc_final: 0.5777 (tmm) REVERT: C 559 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8040 (ttmt) REVERT: A 48 GLU cc_start: 0.8280 (tp30) cc_final: 0.7895 (tp30) REVERT: A 101 GLN cc_start: 0.8625 (mt0) cc_final: 0.8131 (tp40) REVERT: A 191 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8057 (tmmt) REVERT: A 202 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7743 (ttm-80) REVERT: A 261 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 306 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8392 (pp) REVERT: A 331 GLN cc_start: 0.7990 (tm130) cc_final: 0.7388 (tm130) REVERT: A 339 ASP cc_start: 0.7178 (m-30) cc_final: 0.6836 (m-30) REVERT: A 361 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8288 (mpt180) REVERT: A 419 TYR cc_start: 0.7970 (m-80) cc_final: 0.7404 (m-80) REVERT: A 438 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7356 (pp) REVERT: A 474 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7457 (mttm) REVERT: A 557 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8523 (p) REVERT: A 755 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8728 (ttm) REVERT: A 799 GLU cc_start: 0.8346 (tt0) cc_final: 0.7583 (pm20) REVERT: A 853 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 860 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6109 (tt0) REVERT: A 1011 ASN cc_start: 0.8576 (t0) cc_final: 0.7513 (m110) REVERT: A 1072 ILE cc_start: 0.7922 (mm) cc_final: 0.7553 (mt) REVERT: A 1078 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7448 (mpt-90) REVERT: A 1161 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7351 (ttt90) REVERT: A 1186 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6878 (tp) REVERT: A 1312 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6545 (pp20) REVERT: A 1314 CYS cc_start: 0.8230 (OUTLIER) cc_final: 0.6772 (m) REVERT: E 541 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6926 (tppt) REVERT: E 578 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5749 (mp) REVERT: F 603 LEU cc_start: 0.7976 (tp) cc_final: 0.7706 (mm) REVERT: G 652 PHE cc_start: 0.4432 (OUTLIER) cc_final: 0.4155 (p90) outliers start: 94 outliers final: 42 residues processed: 251 average time/residue: 0.6303 time to fit residues: 171.3890 Evaluate side-chains 234 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 777 LYS Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1312 GLU Chi-restraints excluded: chain A residue 1314 CYS Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 577 MET Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Chi-restraints excluded: chain G residue 652 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 137 optimal weight: 0.0370 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN ** A1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125076 restraints weight = 15844.316| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.16 r_work: 0.3349 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12423 Z= 0.115 Angle : 0.477 7.643 16766 Z= 0.248 Chirality : 0.040 0.154 1917 Planarity : 0.004 0.053 2125 Dihedral : 5.418 59.409 1654 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.56 % Allowed : 28.14 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: 1.75 (0.22), residues: 1494 helix: 2.42 (0.19), residues: 826 sheet: -0.23 (0.50), residues: 96 loop : -0.48 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 675 TYR 0.022 0.001 TYR A1214 PHE 0.013 0.001 PHE A 399 TRP 0.014 0.001 TRP A1248 HIS 0.003 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00267 (12423) covalent geometry : angle 0.47683 (16766) hydrogen bonds : bond 0.03531 ( 678) hydrogen bonds : angle 4.04547 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 179 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6720 (mm-30) REVERT: D 577 MET cc_start: 0.6244 (tmm) cc_final: 0.5778 (tmm) REVERT: C 559 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8016 (ttmt) REVERT: A 44 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7912 (mptt) REVERT: A 48 GLU cc_start: 0.8203 (tp30) cc_final: 0.7817 (tp30) REVERT: A 101 GLN cc_start: 0.8619 (mt0) cc_final: 0.8144 (tp40) REVERT: A 191 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8059 (tmmt) REVERT: A 202 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7699 (ttm-80) REVERT: A 261 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8028 (mt) REVERT: A 306 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8324 (pp) REVERT: A 331 GLN cc_start: 0.7930 (tm130) cc_final: 0.7369 (tm130) REVERT: A 339 ASP cc_start: 0.7174 (m-30) cc_final: 0.6813 (m-30) REVERT: A 361 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8166 (mpt180) REVERT: A 381 MET cc_start: 0.8798 (mmt) cc_final: 0.8445 (mmt) REVERT: A 419 TYR cc_start: 0.7953 (m-80) cc_final: 0.7351 (m-80) REVERT: A 438 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7399 (pp) REVERT: A 474 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7370 (mttm) REVERT: A 557 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8363 (p) REVERT: A 755 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8644 (ttm) REVERT: A 799 GLU cc_start: 0.8250 (tt0) cc_final: 0.7572 (pm20) REVERT: A 860 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6093 (tt0) REVERT: A 1011 ASN cc_start: 0.8545 (t0) cc_final: 0.7468 (m110) REVERT: A 1161 ARG cc_start: 0.7937 (mpp80) cc_final: 0.7241 (ttt90) REVERT: A 1186 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6877 (tp) REVERT: F 603 LEU cc_start: 0.7927 (tp) cc_final: 0.7681 (mm) outliers start: 76 outliers final: 31 residues processed: 235 average time/residue: 0.6607 time to fit residues: 168.0318 Evaluate side-chains 216 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 99 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124883 restraints weight = 15836.655| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.16 r_work: 0.3349 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12423 Z= 0.125 Angle : 0.478 7.654 16766 Z= 0.249 Chirality : 0.040 0.168 1917 Planarity : 0.004 0.051 2125 Dihedral : 5.238 57.812 1652 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.21 % Allowed : 27.27 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: 1.77 (0.22), residues: 1494 helix: 2.43 (0.19), residues: 826 sheet: -0.21 (0.50), residues: 96 loop : -0.47 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 675 TYR 0.024 0.001 TYR A1214 PHE 0.014 0.001 PHE A 399 TRP 0.014 0.001 TRP A1248 HIS 0.004 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00293 (12423) covalent geometry : angle 0.47810 (16766) hydrogen bonds : bond 0.03524 ( 678) hydrogen bonds : angle 4.00701 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 181 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6696 (mm-30) REVERT: D 577 MET cc_start: 0.6204 (tmm) cc_final: 0.5724 (tmm) REVERT: C 559 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7997 (ttmt) REVERT: A 44 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7911 (mptt) REVERT: A 101 GLN cc_start: 0.8611 (mt0) cc_final: 0.8141 (tp40) REVERT: A 191 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8053 (tmmt) REVERT: A 202 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7688 (ttm-80) REVERT: A 261 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8009 (mt) REVERT: A 306 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8315 (pp) REVERT: A 331 GLN cc_start: 0.7913 (tm130) cc_final: 0.7318 (tm130) REVERT: A 339 ASP cc_start: 0.7165 (m-30) cc_final: 0.6812 (m-30) REVERT: A 361 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8092 (mpt180) REVERT: A 381 MET cc_start: 0.8808 (mmt) cc_final: 0.8443 (mmt) REVERT: A 419 TYR cc_start: 0.7976 (m-80) cc_final: 0.7376 (m-80) REVERT: A 438 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7433 (pp) REVERT: A 474 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7382 (mttm) REVERT: A 557 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 755 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8686 (ttm) REVERT: A 799 GLU cc_start: 0.8199 (tt0) cc_final: 0.7552 (pm20) REVERT: A 841 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8526 (mtmm) REVERT: A 860 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6085 (tt0) REVERT: A 1011 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7448 (m110) REVERT: A 1078 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7602 (mpt-90) REVERT: A 1161 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7243 (ttt90) REVERT: A 1186 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6648 (tp) REVERT: A 1235 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: E 541 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6879 (tppt) REVERT: F 603 LEU cc_start: 0.7989 (tp) cc_final: 0.7698 (mm) outliers start: 85 outliers final: 38 residues processed: 239 average time/residue: 0.6583 time to fit residues: 170.4288 Evaluate side-chains 232 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 143 optimal weight: 0.0270 chunk 6 optimal weight: 0.7980 chunk 123 optimal weight: 0.0060 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.7056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124949 restraints weight = 15828.984| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.15 r_work: 0.3353 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12423 Z= 0.125 Angle : 0.481 7.446 16766 Z= 0.249 Chirality : 0.040 0.171 1917 Planarity : 0.004 0.053 2125 Dihedral : 5.218 56.568 1652 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 6.21 % Allowed : 27.41 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: 1.78 (0.22), residues: 1494 helix: 2.43 (0.19), residues: 826 sheet: -0.18 (0.50), residues: 96 loop : -0.46 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 675 TYR 0.025 0.001 TYR A1214 PHE 0.014 0.001 PHE A 399 TRP 0.013 0.001 TRP A1248 HIS 0.004 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00295 (12423) covalent geometry : angle 0.48082 (16766) hydrogen bonds : bond 0.03508 ( 678) hydrogen bonds : angle 3.99912 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 180 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6676 (mm-30) REVERT: D 577 MET cc_start: 0.6193 (tmm) cc_final: 0.5714 (tmm) REVERT: C 559 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8000 (ttmt) REVERT: A 44 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7908 (mptt) REVERT: A 48 GLU cc_start: 0.8211 (tp30) cc_final: 0.7816 (tp30) REVERT: A 101 GLN cc_start: 0.8611 (mt0) cc_final: 0.8142 (tp40) REVERT: A 191 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8032 (tmmt) REVERT: A 202 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7704 (ttm-80) REVERT: A 261 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 306 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8309 (pp) REVERT: A 331 GLN cc_start: 0.7911 (tm130) cc_final: 0.7320 (tm130) REVERT: A 339 ASP cc_start: 0.7182 (m-30) cc_final: 0.6823 (m-30) REVERT: A 361 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8080 (mpt180) REVERT: A 419 TYR cc_start: 0.7991 (m-80) cc_final: 0.7326 (m-80) REVERT: A 474 LYS cc_start: 0.7630 (mtmm) cc_final: 0.7389 (mttm) REVERT: A 557 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 735 MET cc_start: 0.8616 (tpt) cc_final: 0.8398 (tpt) REVERT: A 755 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (ttm) REVERT: A 799 GLU cc_start: 0.8206 (tt0) cc_final: 0.7583 (pm20) REVERT: A 860 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6078 (tt0) REVERT: A 1011 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.7445 (m110) REVERT: A 1078 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7597 (mpt-90) REVERT: A 1137 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 1161 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7231 (ttt90) REVERT: A 1186 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6772 (tp) REVERT: A 1235 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6236 (tp30) REVERT: A 1312 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6639 (pp20) REVERT: E 541 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6868 (tppt) REVERT: F 603 LEU cc_start: 0.7999 (tp) cc_final: 0.7731 (mm) outliers start: 85 outliers final: 42 residues processed: 242 average time/residue: 0.6321 time to fit residues: 165.5834 Evaluate side-chains 236 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1312 GLU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124786 restraints weight = 15834.475| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.16 r_work: 0.3348 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12423 Z= 0.128 Angle : 0.484 7.575 16766 Z= 0.250 Chirality : 0.041 0.173 1917 Planarity : 0.004 0.050 2125 Dihedral : 5.218 55.561 1652 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.58 % Allowed : 27.49 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.22), residues: 1494 helix: 2.42 (0.19), residues: 826 sheet: -0.16 (0.50), residues: 96 loop : -0.48 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 675 TYR 0.026 0.001 TYR A1214 PHE 0.014 0.001 PHE A 399 TRP 0.012 0.001 TRP A1248 HIS 0.005 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00304 (12423) covalent geometry : angle 0.48401 (16766) hydrogen bonds : bond 0.03521 ( 678) hydrogen bonds : angle 3.99821 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 180 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6666 (mm-30) REVERT: D 577 MET cc_start: 0.6293 (tmm) cc_final: 0.5804 (tmm) REVERT: C 559 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8007 (ttmt) REVERT: A 44 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7902 (mptt) REVERT: A 101 GLN cc_start: 0.8611 (mt0) cc_final: 0.8145 (tp40) REVERT: A 163 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: A 191 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8033 (tmmt) REVERT: A 202 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7716 (ttm-80) REVERT: A 306 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8310 (pp) REVERT: A 331 GLN cc_start: 0.7929 (tm130) cc_final: 0.7331 (tm130) REVERT: A 339 ASP cc_start: 0.7175 (m-30) cc_final: 0.6812 (m-30) REVERT: A 361 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8076 (mpt180) REVERT: A 381 MET cc_start: 0.8758 (mmt) cc_final: 0.8426 (mmt) REVERT: A 419 TYR cc_start: 0.7987 (m-80) cc_final: 0.7335 (m-80) REVERT: A 474 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7414 (mttm) REVERT: A 557 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 719 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 755 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8693 (ttm) REVERT: A 799 GLU cc_start: 0.8215 (tt0) cc_final: 0.7595 (pm20) REVERT: A 860 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6089 (tt0) REVERT: A 1011 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.7433 (m110) REVERT: A 1072 ILE cc_start: 0.7910 (mm) cc_final: 0.7600 (mt) REVERT: A 1078 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7618 (mpt-90) REVERT: A 1137 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 1161 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7242 (ttt90) REVERT: A 1186 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6771 (tp) REVERT: A 1235 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6251 (tp30) REVERT: A 1312 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6652 (pp20) REVERT: E 541 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6892 (tppt) REVERT: F 603 LEU cc_start: 0.7869 (tp) cc_final: 0.7643 (mm) outliers start: 90 outliers final: 42 residues processed: 248 average time/residue: 0.6489 time to fit residues: 173.9322 Evaluate side-chains 236 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1312 GLU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN A 968 ASN ** A1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.124000 restraints weight = 15741.588| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.14 r_work: 0.3336 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12423 Z= 0.150 Angle : 0.506 7.607 16766 Z= 0.262 Chirality : 0.042 0.183 1917 Planarity : 0.004 0.051 2125 Dihedral : 5.120 49.109 1650 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.77 % Allowed : 28.29 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: 1.68 (0.22), residues: 1494 helix: 2.36 (0.19), residues: 826 sheet: -0.27 (0.50), residues: 96 loop : -0.49 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 675 TYR 0.027 0.001 TYR A1214 PHE 0.016 0.001 PHE A 399 TRP 0.011 0.001 TRP A1248 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00360 (12423) covalent geometry : angle 0.50617 (16766) hydrogen bonds : bond 0.03709 ( 678) hydrogen bonds : angle 4.05583 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 180 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6756 (mm-30) REVERT: D 577 MET cc_start: 0.6279 (tmm) cc_final: 0.5891 (tmm) REVERT: C 559 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7981 (ttmt) REVERT: A 44 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7911 (mptt) REVERT: A 48 GLU cc_start: 0.8239 (tp30) cc_final: 0.7847 (tp30) REVERT: A 101 GLN cc_start: 0.8621 (mt0) cc_final: 0.8148 (tp40) REVERT: A 202 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7714 (ttm-80) REVERT: A 261 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7968 (mt) REVERT: A 306 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8333 (pp) REVERT: A 331 GLN cc_start: 0.7933 (tm130) cc_final: 0.7321 (tm130) REVERT: A 339 ASP cc_start: 0.7158 (m-30) cc_final: 0.6807 (m-30) REVERT: A 361 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8097 (mpt180) REVERT: A 381 MET cc_start: 0.8787 (mmt) cc_final: 0.8446 (mmt) REVERT: A 419 TYR cc_start: 0.8002 (m-80) cc_final: 0.7340 (m-80) REVERT: A 474 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7429 (mttm) REVERT: A 557 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 719 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8239 (tt) REVERT: A 755 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8716 (ttm) REVERT: A 799 GLU cc_start: 0.8216 (tt0) cc_final: 0.7611 (pm20) REVERT: A 860 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6101 (tt0) REVERT: A 973 LEU cc_start: 0.8108 (tm) cc_final: 0.7889 (tp) REVERT: A 1011 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7437 (m110) REVERT: A 1072 ILE cc_start: 0.7898 (mm) cc_final: 0.7600 (mt) REVERT: A 1078 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7495 (mpt-90) REVERT: A 1137 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 1161 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7259 (ttt90) REVERT: A 1186 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6832 (tp) REVERT: A 1235 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6369 (tp30) REVERT: A 1312 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6648 (pp20) REVERT: E 541 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6916 (tppt) outliers start: 79 outliers final: 44 residues processed: 241 average time/residue: 0.6652 time to fit residues: 173.3234 Evaluate side-chains 234 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1312 GLU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 124 optimal weight: 7.9990 chunk 20 optimal weight: 0.0670 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN ** A1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125171 restraints weight = 15733.523| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.15 r_work: 0.3356 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12423 Z= 0.121 Angle : 0.489 7.634 16766 Z= 0.253 Chirality : 0.041 0.179 1917 Planarity : 0.004 0.049 2125 Dihedral : 5.049 49.414 1650 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.12 % Allowed : 29.46 % Favored : 65.42 % 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 aren not related in a simple way. whole: 1.76 (0.22), residues: 1494 helix: 2.41 (0.19), residues: 832 sheet: -0.21 (0.50), residues: 96 loop : -0.48 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 675 TYR 0.027 0.001 TYR A1214 PHE 0.013 0.001 PHE A 399 TRP 0.014 0.001 TRP A1248 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00282 (12423) covalent geometry : angle 0.48910 (16766) hydrogen bonds : bond 0.03463 ( 678) hydrogen bonds : angle 3.99386 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6761 (mm-30) REVERT: D 577 MET cc_start: 0.6230 (tmm) cc_final: 0.5731 (tmm) REVERT: C 559 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8009 (ttmt) REVERT: A 44 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7883 (mptt) REVERT: A 101 GLN cc_start: 0.8599 (mt0) cc_final: 0.8140 (tp40) REVERT: A 202 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7717 (ttm-80) REVERT: A 261 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7961 (mt) REVERT: A 306 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8319 (pp) REVERT: A 331 GLN cc_start: 0.7935 (tm130) cc_final: 0.7338 (tm130) REVERT: A 339 ASP cc_start: 0.7179 (m-30) cc_final: 0.6824 (m-30) REVERT: A 361 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8033 (mpt180) REVERT: A 381 MET cc_start: 0.8766 (mmt) cc_final: 0.8425 (mmt) REVERT: A 419 TYR cc_start: 0.7985 (m-80) cc_final: 0.7344 (m-80) REVERT: A 474 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7422 (mttm) REVERT: A 557 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 755 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8696 (ttm) REVERT: A 799 GLU cc_start: 0.8219 (tt0) cc_final: 0.7579 (pm20) REVERT: A 860 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: A 973 LEU cc_start: 0.8086 (tm) cc_final: 0.7878 (tp) REVERT: A 1011 ASN cc_start: 0.8519 (t0) cc_final: 0.7420 (m110) REVERT: A 1072 ILE cc_start: 0.7892 (mm) cc_final: 0.7604 (mt) REVERT: A 1078 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7578 (mpt-90) REVERT: A 1137 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 1161 ARG cc_start: 0.7923 (mpp80) cc_final: 0.7247 (ttt90) REVERT: A 1186 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6853 (tp) REVERT: A 1235 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6262 (tp30) REVERT: E 541 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6946 (tppt) REVERT: G 637 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6460 (pp) outliers start: 70 outliers final: 40 residues processed: 230 average time/residue: 0.6169 time to fit residues: 153.6929 Evaluate side-chains 227 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 577 MET Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN ** A1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124884 restraints weight = 15821.721| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.15 r_work: 0.3353 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12423 Z= 0.125 Angle : 0.495 7.540 16766 Z= 0.255 Chirality : 0.041 0.184 1917 Planarity : 0.004 0.050 2125 Dihedral : 5.042 49.336 1650 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 4.75 % Allowed : 29.82 % Favored : 65.42 % 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 aren not related in a simple way. whole: 1.75 (0.22), residues: 1494 helix: 2.40 (0.19), residues: 832 sheet: -0.18 (0.50), residues: 96 loop : -0.49 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 675 TYR 0.027 0.001 TYR A1214 PHE 0.014 0.001 PHE A 399 TRP 0.013 0.001 TRP A1248 HIS 0.005 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00294 (12423) covalent geometry : angle 0.49521 (16766) hydrogen bonds : bond 0.03486 ( 678) hydrogen bonds : angle 3.99731 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 176 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6751 (mm-30) REVERT: D 577 MET cc_start: 0.6223 (tmm) cc_final: 0.5840 (tmm) REVERT: C 559 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7977 (ttmt) REVERT: A 44 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7885 (mptt) REVERT: A 101 GLN cc_start: 0.8621 (mt0) cc_final: 0.8147 (tp40) REVERT: A 202 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7718 (ttm-80) REVERT: A 261 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 306 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 331 GLN cc_start: 0.7929 (tm130) cc_final: 0.7331 (tm130) REVERT: A 339 ASP cc_start: 0.7098 (m-30) cc_final: 0.6756 (m-30) REVERT: A 361 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8016 (mpt180) REVERT: A 381 MET cc_start: 0.8765 (mmt) cc_final: 0.8409 (mmt) REVERT: A 419 TYR cc_start: 0.7988 (m-80) cc_final: 0.7277 (m-80) REVERT: A 474 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7418 (mttm) REVERT: A 557 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8333 (p) REVERT: A 755 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8703 (ttm) REVERT: A 799 GLU cc_start: 0.8212 (tt0) cc_final: 0.7580 (pm20) REVERT: A 860 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6058 (tt0) REVERT: A 973 LEU cc_start: 0.8052 (tm) cc_final: 0.7846 (tp) REVERT: A 1011 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7420 (m110) REVERT: A 1072 ILE cc_start: 0.7899 (mm) cc_final: 0.7607 (mt) REVERT: A 1078 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7543 (mpt-90) REVERT: A 1137 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7843 (mp) REVERT: A 1161 ARG cc_start: 0.7929 (mpp80) cc_final: 0.7254 (ttt90) REVERT: A 1186 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6835 (tp) REVERT: A 1235 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6295 (tp30) REVERT: A 1312 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6658 (pp20) REVERT: E 541 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6951 (tppt) REVERT: G 637 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6460 (pp) outliers start: 65 outliers final: 41 residues processed: 226 average time/residue: 0.6611 time to fit residues: 161.6858 Evaluate side-chains 228 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1312 GLU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 577 MET Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 647 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 105 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 0.0870 chunk 137 optimal weight: 0.0470 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 511 ASN A 968 ASN ** A1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121568 restraints weight = 15611.590| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.21 r_work: 0.3311 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12423 Z= 0.105 Angle : 0.486 7.494 16766 Z= 0.248 Chirality : 0.040 0.188 1917 Planarity : 0.004 0.048 2125 Dihedral : 4.946 49.462 1650 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 4.39 % Allowed : 30.48 % Favored : 65.13 % 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 aren not related in a simple way. whole: 1.86 (0.23), residues: 1494 helix: 2.49 (0.19), residues: 832 sheet: -0.13 (0.51), residues: 96 loop : -0.45 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 675 TYR 0.026 0.001 TYR A1214 PHE 0.013 0.001 PHE A 399 TRP 0.015 0.001 TRP A1248 HIS 0.006 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00238 (12423) covalent geometry : angle 0.48602 (16766) hydrogen bonds : bond 0.03251 ( 678) hydrogen bonds : angle 3.91971 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5034.25 seconds wall clock time: 86 minutes 43.50 seconds (5203.50 seconds total)