Starting phenix.real_space_refine on Mon Sep 14 13:28:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vpd_32063/09_2026/7vpd_32063.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 168 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 18840 2.51 5 N 5525 2.21 5 O 6280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30924 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1730 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "S" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12673 SG CYS D 60 70.585 109.436 126.834 1.00109.51 S ATOM 12691 SG CYS D 62 69.748 111.035 129.757 1.00113.61 S ATOM 12800 SG CYS D 75 73.483 110.145 129.466 1.00117.90 S ATOM 12826 SG CYS D 78 71.522 107.311 129.927 1.00107.59 S ATOM 19225 SG CYS D 886 110.165 61.407 99.007 1.00 90.51 S ATOM 19789 SG CYS D 962 106.447 61.400 100.326 1.00 82.70 S ATOM 19837 SG CYS D 969 107.029 62.860 96.936 1.00 83.21 S ATOM 19856 SG CYS D 972 107.419 59.275 97.497 1.00 78.77 S ATOM 25721 SG CYS M 90 56.238 156.211 46.011 1.00236.14 S ATOM 25743 SG CYS M 93 53.167 157.823 47.748 1.00237.18 S ATOM 26016 SG CYS M 130 52.799 154.867 45.352 1.00236.71 S ATOM 26035 SG CYS M 133 53.725 158.382 44.112 1.00234.73 S ATOM 25635 SG CYS M 79 58.722 145.036 56.738 1.00239.38 S ATOM 26705 SG CYS N 90 84.033 135.641 47.758 1.00233.86 S ATOM 26727 SG CYS N 93 87.790 134.905 47.356 1.00230.63 S ATOM 27000 SG CYS N 130 85.120 132.758 45.624 1.00232.87 S ATOM 27019 SG CYS N 133 85.655 132.521 49.332 1.00231.61 S ATOM 26619 SG CYS N 79 80.569 142.948 34.348 1.00238.35 S Time building chain proxies: 6.34, per 1000 atoms: 0.21 Number of scatterers: 30924 At special positions: 0 Unit cell: (131.25, 199.5, 215.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 102 16.00 P 168 15.00 Mg 1 11.99 O 6280 8.00 N 5525 7.00 C 18840 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: 2.61 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 24 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6508 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 42 sheets defined 45.0% alpha, 13.3% beta 68 base pairs and 124 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.621A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.530A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.509A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.880A pdb=" N LEU B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.590A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.529A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 221 through 229 removed outlier: 4.009A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.801A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.563A pdb=" N GLY C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.972A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 4.099A pdb=" N PHE C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.731A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.029A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 574 through 580 removed outlier: 4.116A pdb=" N ILE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.780A pdb=" N ALA C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.110A pdb=" N ASP C 719 " --> pdb=" O ASN C 716 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 720 " --> pdb=" O TYR C 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 716 through 720' Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.184A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.687A pdb=" N LEU C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 Processing helix chain 'C' and resid 1021 through 1026 Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.665A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.262A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.800A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.545A pdb=" N ASP D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 228 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.540A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.832A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.555A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.990A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.867A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.648A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.815A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 3.530A pdb=" N TYR D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 529 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.631A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.878A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.608A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.611A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 916 removed outlier: 3.663A pdb=" N SER D 914 " --> pdb=" O ASP D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.557A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.561A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.549A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1107 removed outlier: 3.538A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1129 removed outlier: 4.182A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.937A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1208 Processing helix chain 'D' and resid 1213 through 1223 Processing helix chain 'D' and resid 1231 through 1237 removed outlier: 3.668A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 removed outlier: 3.523A pdb=" N LYS D1262 " --> pdb=" O THR D1258 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 24 Processing helix chain 'E' and resid 26 through 45 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.565A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 removed outlier: 4.128A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 292 removed outlier: 4.542A pdb=" N ARG F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.624A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 476 Processing helix chain 'F' and resid 482 through 497 Processing helix chain 'F' and resid 498 through 499 No H-bonds generated for 'chain 'F' and resid 498 through 499' Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 510 removed outlier: 4.233A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR F 509 " --> pdb=" O VAL F 505 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.512A pdb=" N VAL M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.952A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.226A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.137A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 255 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 271 through 278 Processing helix chain 'S' and resid 279 through 286 Processing helix chain 'S' and resid 290 through 304 removed outlier: 3.774A pdb=" N MET S 304 " --> pdb=" O LYS S 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.300A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.754A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.678A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP B 188 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP B 190 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 175 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 7.538A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.056A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.391A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 100 removed outlier: 5.467A pdb=" N LEU C 93 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR C 128 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE C 95 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLU C 126 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP C 97 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 142 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 134 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 364 removed outlier: 6.203A pdb=" N SER C 165 " --> pdb=" O ASN C 442 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.698A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.753A pdb=" N ARG C 491 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.753A pdb=" N ARG C 491 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 5.344A pdb=" N VAL C 636 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR C 647 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 638 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.588A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 746 removed outlier: 3.725A pdb=" N HIS C 741 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 857 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.668A pdb=" N GLU C 754 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AC8, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.607A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1052 through 1053 removed outlier: 3.638A pdb=" N LYS D 420 " --> pdb=" O PHE C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1121 through 1123 removed outlier: 3.660A pdb=" N LEU D 10 " --> pdb=" O ASP D1226 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AD3, first strand: chain 'D' and resid 135 through 139 removed outlier: 5.343A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 336 through 337 Processing sheet with id=AD5, first strand: chain 'D' and resid 430 through 432 Processing sheet with id=AD6, first strand: chain 'D' and resid 443 through 444 removed outlier: 5.885A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AD9, first strand: chain 'D' and resid 892 through 894 removed outlier: 4.228A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1070 through 1073 Processing sheet with id=AE2, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE3, first strand: chain 'D' and resid 1254 through 1257 removed outlier: 3.507A pdb=" N GLU E 83 " --> pdb=" O ARG D1254 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 65 through 68 Processing sheet with id=AE5, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.462A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE N 127 " --> pdb=" O ALA M 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR M 123 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU N 125 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS N 87 " --> pdb=" O ILE N 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 30 through 31 1267 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 177 hydrogen bonds 350 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 124 stacking parallelities Total time for adding SS restraints: 8.21 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8212 1.33 - 1.45: 6095 1.45 - 1.58: 16956 1.58 - 1.70: 334 1.70 - 1.82: 178 Bond restraints: 31775 Sorted by residual: bond pdb=" C1' DC O 8 " pdb=" N1 DC O 8 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.29e+01 bond pdb=" C5' DG O 30 " pdb=" C4' DG O 30 " ideal model delta sigma weight residual 1.512 1.549 -0.037 7.00e-03 2.04e+04 2.81e+01 bond pdb=" C1' DC O 83 " pdb=" N1 DC O 83 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" C3' DT O 19 " pdb=" C2' DT O 19 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.25e+01 bond pdb=" C1' DC O 29 " pdb=" N1 DC O 29 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.12e+01 ... (remaining 31770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 42003 1.93 - 3.86: 1423 3.86 - 5.80: 225 5.80 - 7.73: 41 7.73 - 9.66: 7 Bond angle restraints: 43699 Sorted by residual: angle pdb=" N GLU F 412 " pdb=" CA GLU F 412 " pdb=" C GLU F 412 " ideal model delta sigma weight residual 111.36 103.98 7.38 1.09e+00 8.42e-01 4.58e+01 angle pdb=" N ARG D 67 " pdb=" CA ARG D 67 " pdb=" C ARG D 67 " ideal model delta sigma weight residual 110.43 118.91 -8.48 1.31e+00 5.83e-01 4.19e+01 angle pdb=" N GLN C 421 " pdb=" CA GLN C 421 " pdb=" C GLN C 421 " ideal model delta sigma weight residual 113.20 105.89 7.31 1.21e+00 6.83e-01 3.65e+01 angle pdb=" N LYS D 66 " pdb=" CA LYS D 66 " pdb=" C LYS D 66 " ideal model delta sigma weight residual 111.36 117.30 -5.94 1.09e+00 8.42e-01 2.97e+01 angle pdb=" N SER C 822 " pdb=" CA SER C 822 " pdb=" C SER C 822 " ideal model delta sigma weight residual 110.35 117.51 -7.16 1.36e+00 5.41e-01 2.77e+01 ... (remaining 43694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 17837 35.89 - 71.78: 1060 71.78 - 107.67: 32 107.67 - 143.56: 7 143.56 - 179.45: 13 Dihedral angle restraints: 18949 sinusoidal: 8840 harmonic: 10109 Sorted by residual: dihedral pdb=" CA ALA C 907 " pdb=" C ALA C 907 " pdb=" N VAL C 908 " pdb=" CA VAL C 908 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA HIS F 354 " pdb=" C HIS F 354 " pdb=" N MET F 355 " pdb=" CA MET F 355 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C4' DT P 76 " pdb=" C3' DT P 76 " pdb=" O3' DT P 76 " pdb=" P DG P 77 " ideal model delta sinusoidal sigma weight residual -140.00 39.45 -179.45 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 18946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3916 0.055 - 0.109: 769 0.109 - 0.164: 257 0.164 - 0.218: 20 0.218 - 0.273: 7 Chirality restraints: 4969 Sorted by residual: chirality pdb=" CA ARG D 67 " pdb=" N ARG D 67 " pdb=" C ARG D 67 " pdb=" CB ARG D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE D 846 " pdb=" N ILE D 846 " pdb=" C ILE D 846 " pdb=" CB ILE D 846 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE D 880 " pdb=" N ILE D 880 " pdb=" C ILE D 880 " pdb=" CB ILE D 880 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4966 not shown) Planarity restraints: 5138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 576 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO D 577 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 462 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO C 463 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 494 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO D 495 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 495 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 495 " 0.033 5.00e-02 4.00e+02 ... (remaining 5135 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 289 2.56 - 3.15: 26526 3.15 - 3.73: 52307 3.73 - 4.32: 67604 4.32 - 4.90: 107817 Nonbonded interactions: 254543 Sorted by model distance: nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.979 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.998 2.230 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.072 2.230 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D1401 " model vdw 2.081 2.170 nonbonded pdb=" O GLU M 27 " pdb=" NE ARG M 77 " model vdw 2.198 3.120 ... (remaining 254538 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 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.660 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 35.090 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.005 0.080 31803 Z= 0.357 Angle : 0.838 15.531 43723 Z= 0.525 Chirality : 0.051 0.273 4969 Planarity : 0.005 0.086 5138 Dihedral : 20.159 179.445 12441 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.44 % Allowed : 19.79 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3513 helix: 1.08 (0.14), residues: 1405 sheet: -1.02 (0.25), residues: 411 loop : -0.67 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 239 TYR 0.034 0.001 TYR E 32 PHE 0.034 0.002 PHE D 226 TRP 0.009 0.002 TRP D 718 HIS 0.020 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.36 (31775) covalent geometry : angle 0.82519 / 0.52 (43699) hydrogen bonds : bond 0.14599 / 9.51 ( 1443) hydrogen bonds : angle 5.87951 / 4.12 ( 3941) metal coordination : bond 0.00473 / 0.27 ( 28) metal coordination : angle 6.30105 / 3.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 391 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6534 (ttm) cc_final: 0.6199 (mtm) REVERT: A 213 LYS cc_start: 0.9211 (tptp) cc_final: 0.8816 (tmtt) REVERT: B 78 LEU cc_start: 0.8243 (mp) cc_final: 0.7966 (tt) REVERT: C 55 LYS cc_start: 0.8931 (ptpt) cc_final: 0.8683 (ptpp) REVERT: C 648 ASN cc_start: 0.4805 (t0) cc_final: 0.3762 (t0) REVERT: C 821 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8063 (p) REVERT: D 43 LYS cc_start: 0.7818 (tppt) cc_final: 0.7579 (mptt) REVERT: D 312 MET cc_start: 0.8728 (mmt) cc_final: 0.8432 (mmm) REVERT: D 379 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7355 (t0) REVERT: D 405 MET cc_start: 0.7996 (mtt) cc_final: 0.7603 (mtt) REVERT: D 862 THR cc_start: 0.8601 (p) cc_final: 0.8192 (t) REVERT: D 1006 MET cc_start: -0.0174 (mmt) cc_final: -0.1119 (mtm) REVERT: F 260 LEU cc_start: 0.9182 (tp) cc_final: 0.8871 (pp) REVERT: F 276 ASN cc_start: 0.9000 (m110) cc_final: 0.8633 (p0) REVERT: F 283 LEU cc_start: 0.9215 (mt) cc_final: 0.8988 (mt) REVERT: F 324 TYR cc_start: 0.8403 (m-80) cc_final: 0.8119 (m-80) REVERT: F 360 ASN cc_start: 0.9217 (p0) cc_final: 0.8978 (p0) outliers start: 13 outliers final: 2 residues processed: 399 average time/residue: 0.2194 time to fit residues: 136.1983 Evaluate side-chains 315 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 311 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 1190 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 152 ASN B 82 GLN B 152 ASN B 185 GLN C 424 GLN C 913 ASN C 916 GLN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 440 GLN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1210 GLN E 64 HIS F 305 GLN F 468 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.156634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.113617 restraints weight = 78555.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.113704 restraints weight = 52095.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114554 restraints weight = 45357.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.114584 restraints weight = 39470.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115197 restraints weight = 35207.166| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31803 Z= 0.164 Angle : 0.734 12.070 43723 Z= 0.388 Chirality : 0.048 0.374 4969 Planarity : 0.005 0.069 5138 Dihedral : 21.153 179.878 5659 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.44 % Allowed : 18.47 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3513 helix: 1.17 (0.14), residues: 1412 sheet: -0.84 (0.26), residues: 378 loop : -0.58 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 182 TYR 0.033 0.002 TYR E 32 PHE 0.020 0.002 PHE D 226 TRP 0.012 0.001 TRP D 718 HIS 0.010 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (31775) covalent geometry : angle 0.72405 / 0.39 (43699) hydrogen bonds : bond 0.05211 / 3.45 ( 1443) hydrogen bonds : angle 4.67429 / 3.32 ( 3941) metal coordination : bond 0.00645 / 0.38 ( 28) metal coordination : angle 5.06335 / 2.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 362 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 VAL cc_start: 0.7242 (OUTLIER) cc_final: 0.6929 (t) REVERT: A 151 GLN cc_start: 0.6738 (pm20) cc_final: 0.6530 (pm20) REVERT: A 213 LYS cc_start: 0.9186 (tptp) cc_final: 0.8705 (tmtt) REVERT: B 79 ASN cc_start: 0.8667 (m-40) cc_final: 0.8386 (m-40) REVERT: C 55 LYS cc_start: 0.8785 (ptpt) cc_final: 0.8560 (ptpp) REVERT: C 442 ASN cc_start: 0.8725 (t0) cc_final: 0.8399 (t0) REVERT: C 608 GLU cc_start: 0.6945 (tt0) cc_final: 0.6716 (tt0) REVERT: C 648 ASN cc_start: 0.5749 (t0) cc_final: 0.4688 (t0) REVERT: C 710 MET cc_start: 0.8400 (ptm) cc_final: 0.8145 (ptm) REVERT: C 749 LYS cc_start: 0.8636 (tppt) cc_final: 0.8323 (ttmt) REVERT: C 759 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8620 (tp) REVERT: C 803 GLU cc_start: 0.8830 (mp0) cc_final: 0.8452 (mp0) REVERT: C 913 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8055 (p0) REVERT: C 969 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5663 (mm-30) REVERT: D 70 PHE cc_start: 0.8089 (p90) cc_final: 0.7565 (p90) REVERT: D 113 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6972 (ptt180) REVERT: D 296 LEU cc_start: 0.8506 (mt) cc_final: 0.8044 (mt) REVERT: D 344 TYR cc_start: 0.8711 (m-80) cc_final: 0.7964 (m-80) REVERT: D 809 MET cc_start: 0.7112 (ttt) cc_final: 0.6670 (tmm) REVERT: D 861 ARG cc_start: 0.6385 (mmm160) cc_final: 0.6101 (mtp180) REVERT: D 862 THR cc_start: 0.8768 (p) cc_final: 0.8375 (t) REVERT: E 17 ASP cc_start: 0.8322 (p0) cc_final: 0.8066 (p0) REVERT: F 233 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: F 245 PHE cc_start: 0.8031 (m-10) cc_final: 0.7819 (m-10) REVERT: F 276 ASN cc_start: 0.8927 (m110) cc_final: 0.8481 (p0) REVERT: F 283 LEU cc_start: 0.9244 (mt) cc_final: 0.9013 (mt) REVERT: F 324 TYR cc_start: 0.8281 (m-80) cc_final: 0.7998 (m-80) REVERT: F 360 ASN cc_start: 0.9079 (p0) cc_final: 0.8782 (p0) REVERT: F 441 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7578 (pp20) REVERT: N 79 CYS cc_start: 0.4976 (OUTLIER) cc_final: 0.4499 (m) outliers start: 72 outliers final: 26 residues processed: 410 average time/residue: 0.1931 time to fit residues: 127.1587 Evaluate side-chains 344 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 913 ASN Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 101 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 160 optimal weight: 0.0370 chunk 324 optimal weight: 10.0000 chunk 347 optimal weight: 50.0000 chunk 17 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 239 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 HIS ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 ASN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 304 GLN D 416 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.156722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113855 restraints weight = 78615.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.113949 restraints weight = 51510.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.114815 restraints weight = 45636.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.114873 restraints weight = 38761.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.115528 restraints weight = 34667.129| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31803 Z= 0.151 Angle : 0.688 11.788 43723 Z= 0.364 Chirality : 0.047 0.360 4969 Planarity : 0.004 0.056 5138 Dihedral : 21.157 176.977 5654 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.91 % Allowed : 19.59 % Favored : 77.50 % 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 are not related in a simple way. whole: 0.15 (0.14), residues: 3513 helix: 1.18 (0.14), residues: 1422 sheet: -0.71 (0.27), residues: 370 loop : -0.58 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 182 TYR 0.030 0.001 TYR E 32 PHE 0.026 0.002 PHE D1209 TRP 0.013 0.001 TRP D 718 HIS 0.008 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (31775) covalent geometry : angle 0.68007 / 0.36 (43699) hydrogen bonds : bond 0.04590 / 3.04 ( 1443) hydrogen bonds : angle 4.48183 / 3.19 ( 3941) metal coordination : bond 0.00518 / 0.28 ( 28) metal coordination : angle 4.50119 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 332 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.6790 (pm20) cc_final: 0.6503 (pm20) REVERT: A 213 LYS cc_start: 0.9179 (tptp) cc_final: 0.8760 (tmtt) REVERT: B 182 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6150 (tpt90) REVERT: C 209 MET cc_start: 0.8067 (mmp) cc_final: 0.7845 (mmm) REVERT: C 442 ASN cc_start: 0.8708 (t0) cc_final: 0.8360 (t0) REVERT: C 517 LEU cc_start: 0.8142 (mp) cc_final: 0.7584 (mp) REVERT: C 608 GLU cc_start: 0.6959 (tt0) cc_final: 0.6735 (tt0) REVERT: C 648 ASN cc_start: 0.5867 (t0) cc_final: 0.4860 (t0) REVERT: C 710 MET cc_start: 0.8453 (ptm) cc_final: 0.8163 (ptp) REVERT: C 749 LYS cc_start: 0.8603 (tppt) cc_final: 0.8362 (ttmt) REVERT: C 759 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8624 (tp) REVERT: C 803 GLU cc_start: 0.8812 (mp0) cc_final: 0.8508 (mp0) REVERT: C 913 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8188 (p0) REVERT: C 927 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8515 (t) REVERT: C 928 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7502 (mtt90) REVERT: C 1073 LEU cc_start: 0.9283 (mm) cc_final: 0.9068 (mm) REVERT: D 113 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6846 (ptt180) REVERT: D 296 LEU cc_start: 0.8250 (mt) cc_final: 0.7665 (mt) REVERT: D 344 TYR cc_start: 0.8704 (m-80) cc_final: 0.8005 (m-80) REVERT: D 861 ARG cc_start: 0.6413 (mmm160) cc_final: 0.6110 (mtp180) REVERT: D 862 THR cc_start: 0.8776 (p) cc_final: 0.8383 (t) REVERT: F 233 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: F 245 PHE cc_start: 0.7943 (m-10) cc_final: 0.7601 (m-10) REVERT: F 283 LEU cc_start: 0.9221 (mt) cc_final: 0.8977 (mt) REVERT: F 324 TYR cc_start: 0.8234 (m-80) cc_final: 0.7973 (m-80) REVERT: F 360 ASN cc_start: 0.9043 (p0) cc_final: 0.8745 (p0) REVERT: F 479 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6528 (t80) REVERT: N 50 THR cc_start: -0.4371 (OUTLIER) cc_final: -0.4699 (t) REVERT: N 79 CYS cc_start: 0.4925 (OUTLIER) cc_final: 0.4426 (m) outliers start: 86 outliers final: 42 residues processed: 395 average time/residue: 0.1857 time to fit residues: 120.0265 Evaluate side-chains 337 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 913 ASN Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 730 ASP Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 121 optimal weight: 0.0570 chunk 211 optimal weight: 1.9990 chunk 319 optimal weight: 50.0000 chunk 164 optimal weight: 0.0670 chunk 117 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 323 optimal weight: 0.3980 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN C 529 GLN C 913 ASN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 416 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.156000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112884 restraints weight = 78444.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.112889 restraints weight = 52728.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113836 restraints weight = 46499.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113824 restraints weight = 39186.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114529 restraints weight = 35143.322| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31803 Z= 0.169 Angle : 0.698 16.566 43723 Z= 0.365 Chirality : 0.047 0.349 4969 Planarity : 0.004 0.056 5138 Dihedral : 21.155 179.856 5651 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.48 % Allowed : 20.13 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3513 helix: 1.18 (0.14), residues: 1421 sheet: -0.64 (0.26), residues: 391 loop : -0.62 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 182 TYR 0.031 0.002 TYR E 32 PHE 0.027 0.002 PHE D1209 TRP 0.015 0.002 TRP F 333 HIS 0.007 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (31775) covalent geometry : angle 0.69006 / 0.36 (43699) hydrogen bonds : bond 0.04377 / 2.90 ( 1443) hydrogen bonds : angle 4.43684 / 3.16 ( 3941) metal coordination : bond 0.00597 / 0.30 ( 28) metal coordination : angle 4.39967 / 2.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 314 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6450 (pm20) REVERT: A 213 LYS cc_start: 0.9166 (tptp) cc_final: 0.8868 (tmtt) REVERT: B 40 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.7109 (tpp80) REVERT: B 182 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.6176 (tpt90) REVERT: C 94 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6694 (p) REVERT: C 442 ASN cc_start: 0.8782 (t0) cc_final: 0.8411 (t0) REVERT: C 460 ASP cc_start: 0.8248 (t0) cc_final: 0.8026 (t0) REVERT: C 517 LEU cc_start: 0.8293 (mp) cc_final: 0.7736 (mp) REVERT: C 648 ASN cc_start: 0.5880 (t0) cc_final: 0.4814 (t0) REVERT: C 710 MET cc_start: 0.8552 (ptm) cc_final: 0.8282 (ptp) REVERT: C 749 LYS cc_start: 0.8670 (tppt) cc_final: 0.8428 (ttmt) REVERT: C 803 GLU cc_start: 0.8847 (mp0) cc_final: 0.8440 (mp0) REVERT: C 806 LEU cc_start: 0.8956 (mt) cc_final: 0.8675 (mt) REVERT: C 913 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8001 (p0) REVERT: C 1039 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7669 (mm-40) REVERT: D 113 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6943 (ptt180) REVERT: D 296 LEU cc_start: 0.8359 (mt) cc_final: 0.7687 (mt) REVERT: D 670 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7906 (tm-30) REVERT: D 862 THR cc_start: 0.8768 (p) cc_final: 0.8368 (t) REVERT: D 1191 MET cc_start: 0.8869 (pmm) cc_final: 0.8052 (pmm) REVERT: F 245 PHE cc_start: 0.8042 (m-10) cc_final: 0.7637 (m-10) REVERT: F 283 LEU cc_start: 0.9236 (mt) cc_final: 0.9001 (mt) REVERT: F 324 TYR cc_start: 0.8196 (m-80) cc_final: 0.7946 (m-80) REVERT: F 479 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6569 (t80) REVERT: N 50 THR cc_start: -0.4284 (OUTLIER) cc_final: -0.4586 (t) REVERT: N 79 CYS cc_start: 0.4870 (OUTLIER) cc_final: 0.4369 (m) outliers start: 103 outliers final: 61 residues processed: 392 average time/residue: 0.1823 time to fit residues: 117.5445 Evaluate side-chains 351 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 282 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 913 ASN Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 216 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 354 optimal weight: 50.0000 chunk 242 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 363 optimal weight: 40.0000 chunk 292 optimal weight: 0.0050 chunk 179 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 ASN D 94 HIS D 304 GLN D 416 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.155734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112480 restraints weight = 78645.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111080 restraints weight = 54589.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112422 restraints weight = 50343.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.112372 restraints weight = 42524.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113011 restraints weight = 38416.673| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31803 Z= 0.169 Angle : 0.689 13.115 43723 Z= 0.359 Chirality : 0.047 0.394 4969 Planarity : 0.004 0.055 5138 Dihedral : 21.150 175.859 5651 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.32 % Allowed : 21.55 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3513 helix: 1.20 (0.14), residues: 1426 sheet: -0.50 (0.27), residues: 367 loop : -0.63 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 182 TYR 0.032 0.001 TYR E 32 PHE 0.035 0.002 PHE D 248 TRP 0.017 0.002 TRP D 105 HIS 0.007 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (31775) covalent geometry : angle 0.68226 / 0.36 (43699) hydrogen bonds : bond 0.04248 / 2.80 ( 1443) hydrogen bonds : angle 4.38756 / 3.13 ( 3941) metal coordination : bond 0.00613 / 0.30 ( 28) metal coordination : angle 4.30485 / 2.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 296 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.6849 (tmm160) cc_final: 0.6628 (ttp80) REVERT: A 151 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: A 213 LYS cc_start: 0.9162 (tptp) cc_final: 0.8859 (tmtt) REVERT: C 94 THR cc_start: 0.6918 (OUTLIER) cc_final: 0.6613 (p) REVERT: C 442 ASN cc_start: 0.8773 (t0) cc_final: 0.8420 (t0) REVERT: C 460 ASP cc_start: 0.8295 (t0) cc_final: 0.8012 (t0) REVERT: C 517 LEU cc_start: 0.8413 (mp) cc_final: 0.7884 (mp) REVERT: C 648 ASN cc_start: 0.6077 (t0) cc_final: 0.5061 (t0) REVERT: C 710 MET cc_start: 0.8517 (ptm) cc_final: 0.8229 (ptp) REVERT: C 749 LYS cc_start: 0.8697 (tppt) cc_final: 0.8407 (ttmt) REVERT: C 803 GLU cc_start: 0.8866 (mp0) cc_final: 0.8441 (mp0) REVERT: C 806 LEU cc_start: 0.9061 (mt) cc_final: 0.8718 (mt) REVERT: C 913 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8092 (p0) REVERT: D 113 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6937 (ptt180) REVERT: D 670 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 1061 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6201 (p) REVERT: D 1191 MET cc_start: 0.8846 (pmm) cc_final: 0.8146 (pmm) REVERT: D 1236 ILE cc_start: 0.8635 (mm) cc_final: 0.8339 (mt) REVERT: F 245 PHE cc_start: 0.8173 (m-10) cc_final: 0.7743 (m-10) REVERT: F 283 LEU cc_start: 0.9260 (mt) cc_final: 0.9019 (mt) REVERT: F 298 MET cc_start: 0.5234 (tpp) cc_final: 0.4954 (tpp) REVERT: F 324 TYR cc_start: 0.8314 (m-80) cc_final: 0.8029 (m-80) REVERT: F 479 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6677 (t80) REVERT: N 50 THR cc_start: -0.4386 (OUTLIER) cc_final: -0.4713 (t) REVERT: N 79 CYS cc_start: 0.5025 (OUTLIER) cc_final: 0.4518 (m) outliers start: 98 outliers final: 62 residues processed: 370 average time/residue: 0.1903 time to fit residues: 116.7701 Evaluate side-chains 343 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 273 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 913 ASN Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 95 optimal weight: 0.0970 chunk 320 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 267 optimal weight: 0.6980 chunk 98 optimal weight: 0.0370 chunk 144 optimal weight: 0.6980 chunk 245 optimal weight: 8.9990 chunk 338 optimal weight: 8.9990 chunk 269 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN C 913 ASN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1210 GLN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.156884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.113750 restraints weight = 78277.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112747 restraints weight = 52816.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113738 restraints weight = 46588.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114316 restraints weight = 37824.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.114718 restraints weight = 34664.177| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31803 Z= 0.135 Angle : 0.676 13.627 43723 Z= 0.350 Chirality : 0.046 0.363 4969 Planarity : 0.004 0.057 5138 Dihedral : 21.122 176.165 5651 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.84 % Allowed : 22.43 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3513 helix: 1.29 (0.14), residues: 1423 sheet: -0.57 (0.27), residues: 379 loop : -0.56 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 999 TYR 0.028 0.001 TYR E 32 PHE 0.022 0.001 PHE D 248 TRP 0.019 0.001 TRP D 105 HIS 0.008 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (31775) covalent geometry : angle 0.66983 / 0.35 (43699) hydrogen bonds : bond 0.04021 / 2.65 ( 1443) hydrogen bonds : angle 4.30276 / 3.07 ( 3941) metal coordination : bond 0.00421 / 0.22 ( 28) metal coordination : angle 3.98407 / 2.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 315 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9135 (tptp) cc_final: 0.8860 (tmtt) REVERT: C 94 THR cc_start: 0.6989 (OUTLIER) cc_final: 0.6689 (p) REVERT: C 442 ASN cc_start: 0.8746 (t0) cc_final: 0.8367 (t0) REVERT: C 460 ASP cc_start: 0.8220 (t0) cc_final: 0.8009 (t0) REVERT: C 517 LEU cc_start: 0.8346 (mp) cc_final: 0.7838 (mp) REVERT: C 648 ASN cc_start: 0.6143 (t0) cc_final: 0.5105 (t0) REVERT: C 710 MET cc_start: 0.8568 (ptm) cc_final: 0.8302 (ptp) REVERT: C 803 GLU cc_start: 0.8870 (mp0) cc_final: 0.8412 (mp0) REVERT: C 806 LEU cc_start: 0.9070 (mt) cc_final: 0.8695 (mt) REVERT: C 819 ARG cc_start: 0.8274 (tmm-80) cc_final: 0.7942 (tmm-80) REVERT: C 999 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6973 (ttt180) REVERT: D 81 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7409 (tm-30) REVERT: D 113 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6916 (ptt180) REVERT: D 344 TYR cc_start: 0.8709 (m-80) cc_final: 0.8078 (m-80) REVERT: D 670 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7801 (tm-30) REVERT: D 862 THR cc_start: 0.8622 (p) cc_final: 0.8206 (t) REVERT: D 1191 MET cc_start: 0.8772 (pmm) cc_final: 0.8007 (pmm) REVERT: F 283 LEU cc_start: 0.9241 (mt) cc_final: 0.9014 (mt) REVERT: F 298 MET cc_start: 0.5072 (tpp) cc_final: 0.4818 (tpp) REVERT: F 324 TYR cc_start: 0.8257 (m-80) cc_final: 0.7949 (m-80) REVERT: F 441 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7574 (pp20) REVERT: F 479 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6699 (t80) REVERT: N 50 THR cc_start: -0.4487 (OUTLIER) cc_final: -0.4796 (t) REVERT: N 79 CYS cc_start: 0.4990 (OUTLIER) cc_final: 0.4494 (m) outliers start: 84 outliers final: 53 residues processed: 378 average time/residue: 0.1891 time to fit residues: 118.0629 Evaluate side-chains 340 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1210 GLN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 169 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 342 optimal weight: 50.0000 chunk 254 optimal weight: 2.9990 chunk 316 optimal weight: 0.8980 chunk 349 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 358 HIS ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1210 GLN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.154202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.110594 restraints weight = 78776.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.109263 restraints weight = 55371.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110300 restraints weight = 52390.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.110470 restraints weight = 44168.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110993 restraints weight = 39568.003| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31803 Z= 0.225 Angle : 0.721 15.137 43723 Z= 0.374 Chirality : 0.048 0.358 4969 Planarity : 0.004 0.055 5138 Dihedral : 21.126 175.925 5651 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.42 % Allowed : 22.53 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3513 helix: 1.18 (0.14), residues: 1428 sheet: -0.60 (0.27), residues: 386 loop : -0.60 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 757 TYR 0.036 0.002 TYR E 32 PHE 0.025 0.002 PHE D 248 TRP 0.026 0.002 TRP C 231 HIS 0.006 0.001 HIS C 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (31775) covalent geometry : angle 0.71383 / 0.37 (43699) hydrogen bonds : bond 0.04278 / 2.84 ( 1443) hydrogen bonds : angle 4.41249 / 3.14 ( 3941) metal coordination : bond 0.00794 / 0.36 ( 28) metal coordination : angle 4.29095 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 290 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7256 (ttm) cc_final: 0.6945 (mtm) REVERT: A 213 LYS cc_start: 0.9183 (tptp) cc_final: 0.8877 (tmtt) REVERT: C 94 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6820 (p) REVERT: C 442 ASN cc_start: 0.8851 (t0) cc_final: 0.8526 (t0) REVERT: C 460 ASP cc_start: 0.8391 (t0) cc_final: 0.8189 (t0) REVERT: C 499 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: C 517 LEU cc_start: 0.8654 (mp) cc_final: 0.8170 (mp) REVERT: C 648 ASN cc_start: 0.6238 (t0) cc_final: 0.5087 (t0) REVERT: C 710 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8248 (ptp) REVERT: C 803 GLU cc_start: 0.8910 (mp0) cc_final: 0.8351 (mp0) REVERT: C 806 LEU cc_start: 0.9161 (mt) cc_final: 0.8772 (mt) REVERT: C 819 ARG cc_start: 0.8380 (tmm-80) cc_final: 0.7993 (tmm-80) REVERT: D 242 ARG cc_start: 0.8698 (ptp-170) cc_final: 0.8336 (ptp-170) REVERT: D 296 LEU cc_start: 0.8445 (mt) cc_final: 0.7878 (mt) REVERT: D 670 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 828 PRO cc_start: 0.8779 (Cg_endo) cc_final: 0.8562 (Cg_exo) REVERT: D 1191 MET cc_start: 0.8664 (pmm) cc_final: 0.8063 (pmm) REVERT: F 283 LEU cc_start: 0.9278 (mt) cc_final: 0.9053 (mt) REVERT: F 324 TYR cc_start: 0.8244 (m-80) cc_final: 0.7957 (m-80) REVERT: F 441 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7629 (pp20) REVERT: F 479 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6680 (t80) REVERT: N 50 THR cc_start: -0.4520 (OUTLIER) cc_final: -0.4827 (t) REVERT: N 79 CYS cc_start: 0.4997 (OUTLIER) cc_final: 0.4496 (m) outliers start: 101 outliers final: 77 residues processed: 367 average time/residue: 0.1794 time to fit residues: 109.1342 Evaluate side-chains 358 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 275 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 754 GLN Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 873 VAL Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 276 ASN Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 164 optimal weight: 1.9990 chunk 354 optimal weight: 50.0000 chunk 142 optimal weight: 0.1980 chunk 91 optimal weight: 0.3980 chunk 267 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 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 = 0.4417 r_free = 0.4417 target = 0.156298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.113181 restraints weight = 78859.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111984 restraints weight = 53066.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113360 restraints weight = 48841.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113334 restraints weight = 40841.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114002 restraints weight = 37019.614| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31803 Z= 0.137 Angle : 0.689 15.439 43723 Z= 0.355 Chirality : 0.047 0.350 4969 Planarity : 0.004 0.053 5138 Dihedral : 21.086 176.558 5651 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.77 % Allowed : 23.41 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3513 helix: 1.31 (0.14), residues: 1432 sheet: -0.49 (0.28), residues: 372 loop : -0.54 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 999 TYR 0.027 0.001 TYR E 32 PHE 0.019 0.001 PHE D 248 TRP 0.023 0.002 TRP C 231 HIS 0.005 0.001 HIS D1087 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (31775) covalent geometry : angle 0.68307 / 0.35 (43699) hydrogen bonds : bond 0.03902 / 2.57 ( 1443) hydrogen bonds : angle 4.26981 / 3.05 ( 3941) metal coordination : bond 0.00406 / 0.20 ( 28) metal coordination : angle 3.84260 / 2.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 295 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7117 (ttm) cc_final: 0.6754 (mtm) REVERT: A 213 LYS cc_start: 0.9146 (tptp) cc_final: 0.8930 (tmtt) REVERT: C 94 THR cc_start: 0.7018 (OUTLIER) cc_final: 0.6681 (p) REVERT: C 359 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.5940 (t80) REVERT: C 442 ASN cc_start: 0.8756 (t0) cc_final: 0.8433 (t0) REVERT: C 460 ASP cc_start: 0.8328 (t0) cc_final: 0.8115 (t0) REVERT: C 517 LEU cc_start: 0.8472 (mp) cc_final: 0.7983 (mp) REVERT: C 648 ASN cc_start: 0.6170 (t0) cc_final: 0.5076 (t0) REVERT: C 803 GLU cc_start: 0.8873 (mp0) cc_final: 0.8299 (mp0) REVERT: C 806 LEU cc_start: 0.9150 (mt) cc_final: 0.8746 (mt) REVERT: D 242 ARG cc_start: 0.8638 (ptp-170) cc_final: 0.8350 (ptp-170) REVERT: D 344 TYR cc_start: 0.8698 (m-80) cc_final: 0.8084 (m-80) REVERT: D 670 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7801 (tm-30) REVERT: D 828 PRO cc_start: 0.8706 (Cg_endo) cc_final: 0.8506 (Cg_exo) REVERT: D 862 THR cc_start: 0.8656 (p) cc_final: 0.8223 (t) REVERT: D 1047 ARG cc_start: 0.8215 (mmp-170) cc_final: 0.7623 (mmm160) REVERT: D 1191 MET cc_start: 0.8662 (pmm) cc_final: 0.7910 (pmm) REVERT: F 245 PHE cc_start: 0.8039 (m-10) cc_final: 0.7809 (m-10) REVERT: F 283 LEU cc_start: 0.9258 (mt) cc_final: 0.9023 (mt) REVERT: F 324 TYR cc_start: 0.8216 (m-80) cc_final: 0.7890 (m-80) REVERT: F 441 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7605 (pp20) REVERT: F 479 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6713 (t80) REVERT: N 50 THR cc_start: -0.4243 (OUTLIER) cc_final: -0.4569 (t) REVERT: N 79 CYS cc_start: 0.4976 (OUTLIER) cc_final: 0.4523 (m) outliers start: 82 outliers final: 60 residues processed: 358 average time/residue: 0.1858 time to fit residues: 110.1030 Evaluate side-chains 339 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 754 GLN Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 262 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 92 optimal weight: 0.0770 chunk 227 optimal weight: 0.9990 chunk 299 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 238 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.156360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113576 restraints weight = 78197.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.112043 restraints weight = 52567.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113641 restraints weight = 49001.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.113478 restraints weight = 40250.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.114198 restraints weight = 37024.780| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31803 Z= 0.139 Angle : 0.687 16.275 43723 Z= 0.355 Chirality : 0.046 0.325 4969 Planarity : 0.004 0.052 5138 Dihedral : 21.052 176.691 5651 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.60 % Allowed : 23.99 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3513 helix: 1.31 (0.14), residues: 1430 sheet: -0.47 (0.27), residues: 384 loop : -0.51 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 757 TYR 0.028 0.001 TYR E 32 PHE 0.017 0.001 PHE D 248 TRP 0.033 0.002 TRP C 231 HIS 0.006 0.001 HIS D 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (31775) covalent geometry : angle 0.68122 / 0.36 (43699) hydrogen bonds : bond 0.03877 / 2.56 ( 1443) hydrogen bonds : angle 4.27431 / 3.05 ( 3941) metal coordination : bond 0.00396 / 0.19 ( 28) metal coordination : angle 3.75373 / 2.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7020 (ttm) cc_final: 0.6681 (mtm) REVERT: A 213 LYS cc_start: 0.9144 (tptp) cc_final: 0.8941 (tmtt) REVERT: B 30 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7191 (t80) REVERT: C 52 ASP cc_start: 0.7345 (p0) cc_final: 0.7030 (p0) REVERT: C 94 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6642 (p) REVERT: C 292 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8861 (mmtt) REVERT: C 442 ASN cc_start: 0.8780 (t0) cc_final: 0.8451 (t0) REVERT: C 460 ASP cc_start: 0.8309 (t0) cc_final: 0.8096 (t0) REVERT: C 517 LEU cc_start: 0.8501 (mp) cc_final: 0.8018 (mp) REVERT: C 579 MET cc_start: 0.8484 (mmp) cc_final: 0.8090 (mmt) REVERT: C 648 ASN cc_start: 0.6175 (t0) cc_final: 0.5064 (t0) REVERT: C 803 GLU cc_start: 0.8868 (mp0) cc_final: 0.8297 (mp0) REVERT: C 806 LEU cc_start: 0.9121 (mt) cc_final: 0.8699 (mt) REVERT: D 242 ARG cc_start: 0.8679 (ptp-170) cc_final: 0.8320 (ptp-170) REVERT: D 344 TYR cc_start: 0.8717 (m-80) cc_final: 0.8101 (m-80) REVERT: D 670 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7797 (tm-30) REVERT: D 828 PRO cc_start: 0.8718 (Cg_endo) cc_final: 0.8505 (Cg_exo) REVERT: D 1047 ARG cc_start: 0.8251 (mmp-170) cc_final: 0.7790 (mmm160) REVERT: D 1191 MET cc_start: 0.8696 (pmm) cc_final: 0.8021 (pmm) REVERT: F 276 ASN cc_start: 0.8977 (m110) cc_final: 0.8583 (p0) REVERT: F 283 LEU cc_start: 0.9245 (mt) cc_final: 0.9010 (mt) REVERT: F 324 TYR cc_start: 0.8201 (m-80) cc_final: 0.7872 (m-80) REVERT: F 441 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7605 (pp20) REVERT: F 479 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6739 (t80) REVERT: N 50 THR cc_start: -0.4065 (OUTLIER) cc_final: -0.4371 (t) REVERT: N 79 CYS cc_start: 0.4974 (OUTLIER) cc_final: 0.4540 (m) outliers start: 77 outliers final: 63 residues processed: 347 average time/residue: 0.1877 time to fit residues: 108.3645 Evaluate side-chains 343 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 274 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 126 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 329 optimal weight: 50.0000 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 0.0670 chunk 289 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** 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 = 0.4409 r_free = 0.4409 target = 0.155789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.112689 restraints weight = 77927.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.111107 restraints weight = 52859.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112143 restraints weight = 49495.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112841 restraints weight = 39006.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113050 restraints weight = 35571.245| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31803 Z= 0.158 Angle : 0.717 17.201 43723 Z= 0.365 Chirality : 0.047 0.325 4969 Planarity : 0.004 0.051 5138 Dihedral : 21.050 176.746 5651 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.47 % Allowed : 24.46 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3513 helix: 1.25 (0.14), residues: 1438 sheet: -0.55 (0.27), residues: 387 loop : -0.50 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 757 TYR 0.029 0.001 TYR E 32 PHE 0.024 0.001 PHE A 21 TRP 0.035 0.002 TRP C 231 HIS 0.005 0.001 HIS D 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (31775) covalent geometry : angle 0.70153 / 0.36 (43699) hydrogen bonds : bond 0.03948 / 2.62 ( 1443) hydrogen bonds : angle 4.30117 / 3.07 ( 3941) metal coordination : bond 0.00917 / 0.44 ( 28) metal coordination : angle 6.40505 / 4.78 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 285 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9168 (tptp) cc_final: 0.8964 (tmtt) REVERT: C 52 ASP cc_start: 0.7347 (p0) cc_final: 0.7042 (p0) REVERT: C 94 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6802 (p) REVERT: C 292 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8868 (mmtt) REVERT: C 442 ASN cc_start: 0.8825 (t0) cc_final: 0.8494 (t0) REVERT: C 517 LEU cc_start: 0.8551 (mp) cc_final: 0.8074 (mp) REVERT: C 616 MET cc_start: 0.8220 (ppp) cc_final: 0.7601 (ppp) REVERT: C 648 ASN cc_start: 0.6236 (t0) cc_final: 0.5035 (t0) REVERT: C 710 MET cc_start: 0.8265 (ptm) cc_final: 0.7913 (ptp) REVERT: C 803 GLU cc_start: 0.8866 (mp0) cc_final: 0.8306 (mp0) REVERT: C 806 LEU cc_start: 0.9157 (mt) cc_final: 0.8739 (mt) REVERT: D 113 ARG cc_start: 0.7069 (ptt180) cc_final: 0.6820 (ptt90) REVERT: D 242 ARG cc_start: 0.8688 (ptp-170) cc_final: 0.8326 (ptp-170) REVERT: D 670 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7842 (tm-30) REVERT: D 828 PRO cc_start: 0.8703 (Cg_endo) cc_final: 0.8493 (Cg_exo) REVERT: D 1047 ARG cc_start: 0.8201 (mmp-170) cc_final: 0.7932 (mmp-170) REVERT: D 1191 MET cc_start: 0.8630 (pmm) cc_final: 0.8013 (pmm) REVERT: F 283 LEU cc_start: 0.9248 (mt) cc_final: 0.9016 (mt) REVERT: F 324 TYR cc_start: 0.8207 (m-80) cc_final: 0.7870 (m-80) REVERT: F 441 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7612 (pp20) REVERT: F 479 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6784 (t80) REVERT: N 79 CYS cc_start: 0.5007 (OUTLIER) cc_final: 0.4581 (m) outliers start: 73 outliers final: 66 residues processed: 340 average time/residue: 0.1949 time to fit residues: 110.0113 Evaluate side-chains 343 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 273 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 962 CYS Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 122 optimal weight: 0.9980 chunk 283 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 331 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 364 optimal weight: 50.0000 chunk 339 optimal weight: 9.9990 chunk 359 optimal weight: 50.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.154282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.110959 restraints weight = 78283.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.109552 restraints weight = 54109.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.110861 restraints weight = 51995.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.110844 restraints weight = 42352.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111561 restraints weight = 38302.114| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31803 Z= 0.206 Angle : 0.740 17.653 43723 Z= 0.378 Chirality : 0.048 0.475 4969 Planarity : 0.005 0.053 5138 Dihedral : 21.078 176.670 5651 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.84 % Allowed : 24.05 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3513 helix: 1.15 (0.14), residues: 1437 sheet: -0.58 (0.27), residues: 387 loop : -0.55 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 757 TYR 0.035 0.002 TYR E 32 PHE 0.027 0.002 PHE D1209 TRP 0.037 0.002 TRP C 231 HIS 0.005 0.001 HIS C 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (31775) covalent geometry : angle 0.72702 / 0.38 (43699) hydrogen bonds : bond 0.04113 / 2.73 ( 1443) hydrogen bonds : angle 4.38261 / 3.13 ( 3941) metal coordination : bond 0.00939 / 0.48 ( 28) metal coordination : angle 5.98399 / 4.48 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5204.21 seconds wall clock time: 90 minutes 55.46 seconds (5455.46 seconds total)