Starting phenix.real_space_refine on Thu Jun 26 18:25:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vpd_32063/06_2025/7vpd_32063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vpd_32063/06_2025/7vpd_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_32063/06_2025/7vpd_32063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vpd_32063/06_2025/7vpd_32063.map" model { file = "/net/cci-nas-00/data/ceres_data/7vpd_32063/06_2025/7vpd_32063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vpd_32063/06_2025/7vpd_32063.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.08, per 1000 atoms: 0.62 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: 8.61 Conformation dependent library (CDL) restraints added in 3.8 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: 13.02 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: 18.80 Time building geometry restraints manager: 10.14 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=" O3' DG O 71 " pdb=" P DG O 72 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" C VAL C 825 " pdb=" N PRO C 826 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.34e-02 5.57e+03 6.47e+00 bond pdb=" C HIS D 494 " pdb=" N PRO D 495 " ideal model delta sigma weight residual 1.332 1.361 -0.030 1.26e-02 6.30e+03 5.55e+00 bond pdb=" O3' DG P 22 " pdb=" P DA P 23 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.50e-02 4.44e+03 5.20e+00 bond pdb=" CA SER C 420 " pdb=" C SER C 420 " ideal model delta sigma weight residual 1.520 1.493 0.027 1.21e-02 6.83e+03 5.06e+00 ... (remaining 31770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 42191 1.93 - 3.86: 1258 3.86 - 5.80: 206 5.80 - 7.73: 35 7.73 - 9.66: 9 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=" O3' DC O 23 " pdb=" C3' DC O 23 " pdb=" C2' DC O 23 " ideal model delta sigma weight residual 111.50 103.30 8.20 1.50e+00 4.44e-01 2.99e+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 ... (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: 4001 0.055 - 0.109: 813 0.109 - 0.164: 133 0.164 - 0.218: 14 0.218 - 0.273: 8 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 99.170 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.061 31803 Z= 0.218 Angle : 0.806 15.531 43723 Z= 0.447 Chirality : 0.046 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP D 718 HIS 0.020 0.001 HIS F 499 PHE 0.034 0.002 PHE D 226 TYR 0.034 0.001 TYR E 32 ARG 0.010 0.001 ARG F 239 Details of bonding type rmsd hydrogen bonds : bond 0.14599 ( 1443) hydrogen bonds : angle 5.87951 ( 3941) metal coordination : bond 0.00473 ( 28) metal coordination : angle 6.30105 ( 24) covalent geometry : bond 0.00467 (31775) covalent geometry : angle 0.79233 (43699) *********************** 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 : 3.042 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: 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: 0.3763 (t0) REVERT: C 821 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (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: 0.7358 (t0) REVERT: D 405 MET cc_start: 0.7996 (mtt) cc_final: 0.7602 (mtt) REVERT: D 862 THR cc_start: 0.8601 (p) cc_final: 0.8193 (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 360 ASN cc_start: 0.9217 (p0) cc_final: 0.8977 (p0) outliers start: 13 outliers final: 2 residues processed: 399 average time/residue: 0.5168 time to fit residues: 320.4940 Evaluate side-chains 316 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 312 time to evaluate : 3.274 ------------------------------------------------------------------------------- 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 308 optimal weight: 5.9990 chunk 276 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 286 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 212 optimal weight: 0.0770 chunk 331 optimal weight: 4.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 185 GLN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 440 GLN E 64 HIS F 305 GLN F 468 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.155665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112577 restraints weight = 77855.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112660 restraints weight = 51909.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113530 restraints weight = 45724.966| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31803 Z= 0.179 Angle : 0.690 11.300 43723 Z= 0.362 Chirality : 0.044 0.219 4969 Planarity : 0.005 0.061 5138 Dihedral : 21.108 179.578 5659 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.67 % Allowed : 18.98 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3513 helix: 1.22 (0.14), residues: 1423 sheet: -0.66 (0.27), residues: 358 loop : -0.55 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 718 HIS 0.007 0.001 HIS F 499 PHE 0.020 0.002 PHE D 226 TYR 0.034 0.001 TYR E 32 ARG 0.013 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 1443) hydrogen bonds : angle 4.57176 ( 3941) metal coordination : bond 0.00653 ( 28) metal coordination : angle 5.14762 ( 24) covalent geometry : bond 0.00406 (31775) covalent geometry : angle 0.67940 (43699) *********************** 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 442 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 363 time to evaluate : 3.141 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: 0.6838 (pm20) cc_final: 0.6548 (pm20) REVERT: B 79 ASN cc_start: 0.8526 (m-40) cc_final: 0.8301 (m-40) REVERT: B 182 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.6288 (tpt90) REVERT: C 94 THR cc_start: 0.6931 (OUTLIER) cc_final: 0.6677 (p) REVERT: C 442 ASN cc_start: 0.8712 (t0) cc_final: 0.8348 (t0) REVERT: C 517 LEU cc_start: 0.8182 (mp) cc_final: 0.7707 (mp) REVERT: C 608 GLU cc_start: 0.6946 (tt0) cc_final: 0.6730 (tt0) REVERT: C 648 ASN cc_start: 0.5800 (t0) cc_final: 0.4644 (t0) REVERT: C 710 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8185 (ptp) REVERT: C 749 LYS cc_start: 0.8606 (tppt) cc_final: 0.8340 (ttmt) REVERT: C 759 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 803 GLU cc_start: 0.8767 (mp0) cc_final: 0.8427 (mp0) REVERT: D 70 PHE cc_start: 0.8223 (p90) cc_final: 0.7785 (p90) REVERT: D 113 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7003 (ptt180) REVERT: D 296 LEU cc_start: 0.8514 (mt) cc_final: 0.8043 (mt) REVERT: D 344 TYR cc_start: 0.8736 (m-80) cc_final: 0.8028 (m-80) REVERT: D 379 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7420 (t0) REVERT: D 861 ARG cc_start: 0.6487 (mmm160) cc_final: 0.6147 (mtp180) REVERT: F 245 PHE cc_start: 0.7890 (m-10) cc_final: 0.7580 (m-10) REVERT: F 276 ASN cc_start: 0.8949 (m110) cc_final: 0.8522 (p0) REVERT: F 283 LEU cc_start: 0.9254 (mt) cc_final: 0.9029 (mt) REVERT: F 360 ASN cc_start: 0.9015 (p0) cc_final: 0.8725 (p0) REVERT: F 479 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6950 (t80) REVERT: N 79 CYS cc_start: 0.4814 (OUTLIER) cc_final: 0.4295 (m) outliers start: 79 outliers final: 34 residues processed: 412 average time/residue: 0.4530 time to fit residues: 297.4844 Evaluate side-chains 351 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 309 time to evaluate : 3.100 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 94 THR 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 759 ILE Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 908 VAL 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 C residue 1116 LEU 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 379 ASP 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 626 ASP 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 E residue 32 TYR 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 428 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 479 TYR 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 198 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 258 optimal weight: 0.0980 chunk 105 optimal weight: 0.4980 chunk 360 optimal weight: 20.0000 chunk 310 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 913 ASN C 916 GLN D 304 GLN D 416 ASN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4407 r_free = 0.4407 target = 0.155612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.112617 restraints weight = 78590.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.112174 restraints weight = 51703.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113406 restraints weight = 48132.353| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31803 Z= 0.167 Angle : 0.653 13.783 43723 Z= 0.342 Chirality : 0.043 0.321 4969 Planarity : 0.004 0.057 5138 Dihedral : 21.054 179.881 5658 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.28 % Allowed : 19.89 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3513 helix: 1.24 (0.14), residues: 1427 sheet: -0.58 (0.26), residues: 380 loop : -0.61 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 333 HIS 0.008 0.001 HIS F 499 PHE 0.022 0.002 PHE D1209 TYR 0.032 0.001 TYR E 32 ARG 0.021 0.001 ARG F 313 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 1443) hydrogen bonds : angle 4.40407 ( 3941) metal coordination : bond 0.00631 ( 28) metal coordination : angle 4.33302 ( 24) covalent geometry : bond 0.00384 (31775) covalent geometry : angle 0.64494 (43699) *********************** 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 439 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 342 time to evaluate : 3.725 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 151 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.6367 (pm20) REVERT: A 213 LYS cc_start: 0.9232 (tptp) cc_final: 0.8828 (tmtt) REVERT: B 40 ARG cc_start: 0.7491 (tpp-160) cc_final: 0.7244 (tpt-90) REVERT: B 78 LEU cc_start: 0.8101 (mp) cc_final: 0.7814 (tt) REVERT: B 182 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6348 (tpt90) REVERT: C 94 THR cc_start: 0.6953 (OUTLIER) cc_final: 0.6650 (p) REVERT: C 442 ASN cc_start: 0.8771 (t0) cc_final: 0.8372 (t0) REVERT: C 517 LEU cc_start: 0.8499 (mp) cc_final: 0.7989 (mp) REVERT: C 648 ASN cc_start: 0.5792 (t0) cc_final: 0.4732 (t0) REVERT: C 710 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8163 (ptp) REVERT: C 749 LYS cc_start: 0.8657 (tppt) cc_final: 0.8416 (ttmt) REVERT: C 803 GLU cc_start: 0.8836 (mp0) cc_final: 0.8553 (mp0) REVERT: C 913 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.7694 (p0) REVERT: D 379 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7284 (t0) REVERT: D 670 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7892 (tm-30) REVERT: D 1006 MET cc_start: 0.2249 (mtm) cc_final: 0.1309 (mmt) REVERT: D 1209 PHE cc_start: 0.8296 (t80) cc_final: 0.8000 (t80) REVERT: F 233 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: F 245 PHE cc_start: 0.8072 (m-10) cc_final: 0.7675 (m-10) REVERT: F 283 LEU cc_start: 0.9254 (mt) cc_final: 0.9007 (mt) REVERT: F 360 ASN cc_start: 0.9007 (p0) cc_final: 0.8700 (p0) REVERT: N 79 CYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4413 (m) outliers start: 97 outliers final: 48 residues processed: 409 average time/residue: 0.4285 time to fit residues: 281.4882 Evaluate side-chains 354 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 3.161 ------------------------------------------------------------------------------- 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 41 THR 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 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 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 359 PHE Chi-restraints excluded: chain C residue 450 SER 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 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 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 319 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 ASP 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 823 LYS Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 956 THR 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 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 211 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU 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 120 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 288 optimal weight: 6.9990 chunk 345 optimal weight: 50.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** D 747 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.156431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112978 restraints weight = 79106.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.112192 restraints weight = 52939.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112976 restraints weight = 46258.100| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2153 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= 0.142 Angle : 0.639 11.207 43723 Z= 0.333 Chirality : 0.042 0.318 4969 Planarity : 0.004 0.053 5138 Dihedral : 21.018 179.372 5655 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.38 % Allowed : 20.50 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3513 helix: 1.30 (0.14), residues: 1431 sheet: -0.42 (0.27), residues: 369 loop : -0.58 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 718 HIS 0.006 0.001 HIS F 499 PHE 0.030 0.002 PHE D 248 TYR 0.029 0.001 TYR E 32 ARG 0.010 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 1443) hydrogen bonds : angle 4.29799 ( 3941) metal coordination : bond 0.00457 ( 28) metal coordination : angle 3.95675 ( 24) covalent geometry : bond 0.00324 (31775) covalent geometry : angle 0.63252 (43699) *********************** 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 435 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 335 time to evaluate : 3.490 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: A 213 LYS cc_start: 0.9225 (tptp) cc_final: 0.8862 (tmtt) REVERT: B 40 ARG cc_start: 0.7446 (tpp-160) cc_final: 0.7131 (tpt-90) REVERT: B 78 LEU cc_start: 0.8152 (mp) cc_final: 0.7816 (tt) REVERT: C 442 ASN cc_start: 0.8733 (t0) cc_final: 0.8352 (t0) REVERT: C 517 LEU cc_start: 0.8394 (mp) cc_final: 0.7860 (mp) REVERT: C 648 ASN cc_start: 0.6161 (t0) cc_final: 0.5116 (t0) REVERT: C 710 MET cc_start: 0.8403 (ptm) cc_final: 0.8108 (ptp) REVERT: C 803 GLU cc_start: 0.8897 (mp0) cc_final: 0.8501 (mp0) REVERT: C 806 LEU cc_start: 0.9013 (mt) cc_final: 0.8687 (mt) REVERT: D 69 ARG cc_start: 0.8036 (ptm160) cc_final: 0.7762 (ptm160) REVERT: D 81 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7409 (tm-30) REVERT: D 261 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8947 (mp) REVERT: D 344 TYR cc_start: 0.8742 (m-80) cc_final: 0.8105 (m-80) REVERT: D 379 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7241 (t0) REVERT: D 670 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 1191 MET cc_start: 0.8794 (pmm) cc_final: 0.8105 (pmm) REVERT: F 245 PHE cc_start: 0.8197 (m-10) cc_final: 0.7743 (m-10) REVERT: F 283 LEU cc_start: 0.9268 (mt) cc_final: 0.9016 (mt) REVERT: F 479 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6836 (t80) REVERT: N 79 CYS cc_start: 0.5028 (OUTLIER) cc_final: 0.4528 (m) outliers start: 100 outliers final: 58 residues processed: 412 average time/residue: 0.4349 time to fit residues: 287.8636 Evaluate side-chains 356 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 3.516 ------------------------------------------------------------------------------- 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 37 SER Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 124 VAL 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 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 246 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 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 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 ASP 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 823 LYS Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1145 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 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 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 79 CYS Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 297 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 235 optimal weight: 0.0870 chunk 295 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 chunk 93 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** D 752 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.156966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113830 restraints weight = 78371.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.112749 restraints weight = 51626.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113816 restraints weight = 45544.424| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31803 Z= 0.134 Angle : 0.637 17.171 43723 Z= 0.328 Chirality : 0.042 0.339 4969 Planarity : 0.004 0.050 5138 Dihedral : 20.949 178.793 5653 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.91 % Allowed : 21.68 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3513 helix: 1.37 (0.14), residues: 1428 sheet: -0.42 (0.27), residues: 389 loop : -0.54 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 231 HIS 0.006 0.001 HIS F 499 PHE 0.024 0.001 PHE D1209 TYR 0.027 0.001 TYR E 32 ARG 0.007 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1443) hydrogen bonds : angle 4.22511 ( 3941) metal coordination : bond 0.00395 ( 28) metal coordination : angle 3.73026 ( 24) covalent geometry : bond 0.00304 (31775) covalent geometry : angle 0.63076 (43699) *********************** 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 419 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 333 time to evaluate : 3.192 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: A 136 MET cc_start: 0.7358 (ttm) cc_final: 0.6944 (mtm) REVERT: A 213 LYS cc_start: 0.9156 (tptp) cc_final: 0.8917 (tmtt) REVERT: B 152 ASN cc_start: 0.8616 (m-40) cc_final: 0.8407 (p0) REVERT: C 52 ASP cc_start: 0.7391 (p0) cc_final: 0.7040 (p0) REVERT: C 94 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6802 (p) REVERT: C 442 ASN cc_start: 0.8767 (t0) cc_final: 0.8376 (t0) REVERT: C 460 ASP cc_start: 0.8239 (t0) cc_final: 0.7959 (t0) REVERT: C 517 LEU cc_start: 0.8436 (mp) cc_final: 0.7928 (mp) REVERT: C 648 ASN cc_start: 0.6231 (t0) cc_final: 0.5116 (t0) REVERT: C 710 MET cc_start: 0.8437 (ptm) cc_final: 0.8139 (ptp) REVERT: C 803 GLU cc_start: 0.8955 (mp0) cc_final: 0.8476 (mp0) REVERT: C 806 LEU cc_start: 0.9120 (mt) cc_final: 0.8714 (mt) REVERT: C 913 ASN cc_start: 0.8392 (p0) cc_final: 0.7764 (p0) REVERT: C 1015 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8788 (tp) REVERT: D 69 ARG cc_start: 0.8150 (ptm160) cc_final: 0.7838 (ptm160) REVERT: D 81 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7357 (tm-30) REVERT: D 113 ARG cc_start: 0.6951 (ptt180) cc_final: 0.6540 (mmt-90) REVERT: D 256 MET cc_start: 0.7762 (tpp) cc_final: 0.7502 (tpp) REVERT: D 344 TYR cc_start: 0.8745 (m-80) cc_final: 0.8176 (m-80) REVERT: D 379 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7165 (t0) REVERT: D 670 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7812 (tm-30) REVERT: D 829 ARG cc_start: 0.6267 (tpp80) cc_final: 0.5985 (tpp-160) REVERT: D 1191 MET cc_start: 0.8767 (pmm) cc_final: 0.8064 (pmm) REVERT: D 1217 THR cc_start: 0.8683 (p) cc_final: 0.8382 (p) REVERT: F 283 LEU cc_start: 0.9276 (mt) cc_final: 0.9043 (mt) REVERT: F 298 MET cc_start: 0.5027 (tpp) cc_final: 0.4773 (tpp) REVERT: F 324 TYR cc_start: 0.8327 (m-80) cc_final: 0.8049 (m-80) REVERT: F 441 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7643 (pp20) REVERT: F 479 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6882 (t80) REVERT: N 79 CYS cc_start: 0.5036 (OUTLIER) cc_final: 0.4571 (m) outliers start: 86 outliers final: 57 residues processed: 402 average time/residue: 0.4195 time to fit residues: 273.6209 Evaluate side-chains 354 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 3.513 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 124 VAL 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 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 246 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 545 VAL 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 759 ILE Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL 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 379 ASP 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 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 1131 SER 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 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 348 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 479 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 297 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 334 optimal weight: 40.0000 chunk 225 optimal weight: 0.8980 chunk 10 optimal weight: 0.0060 chunk 140 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 304 GLN ** D 752 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.156388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.113035 restraints weight = 78634.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.111951 restraints weight = 52022.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112855 restraints weight = 48069.521| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31803 Z= 0.149 Angle : 0.654 16.847 43723 Z= 0.333 Chirality : 0.043 0.373 4969 Planarity : 0.004 0.083 5138 Dihedral : 20.939 179.133 5653 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.25 % Allowed : 22.46 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3513 helix: 1.37 (0.14), residues: 1438 sheet: -0.46 (0.27), residues: 405 loop : -0.55 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 231 HIS 0.004 0.001 HIS D1010 PHE 0.020 0.001 PHE D1209 TYR 0.030 0.001 TYR E 32 ARG 0.009 0.000 ARG C 999 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 1443) hydrogen bonds : angle 4.18166 ( 3941) metal coordination : bond 0.01012 ( 28) metal coordination : angle 6.04681 ( 24) covalent geometry : bond 0.00341 (31775) covalent geometry : angle 0.63910 (43699) *********************** 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 401 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 305 time to evaluate : 3.513 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: A 213 LYS cc_start: 0.9122 (tptp) cc_final: 0.8908 (tmtt) REVERT: B 152 ASN cc_start: 0.8631 (m-40) cc_final: 0.8371 (p0) REVERT: C 52 ASP cc_start: 0.7325 (p0) cc_final: 0.6995 (p0) REVERT: C 94 THR cc_start: 0.6998 (OUTLIER) cc_final: 0.6670 (p) REVERT: C 442 ASN cc_start: 0.8805 (t0) cc_final: 0.8414 (t0) REVERT: C 460 ASP cc_start: 0.8222 (t0) cc_final: 0.7969 (t0) REVERT: C 499 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: C 517 LEU cc_start: 0.8485 (mp) cc_final: 0.8025 (mp) REVERT: C 648 ASN cc_start: 0.6197 (t0) cc_final: 0.5068 (t0) REVERT: C 710 MET cc_start: 0.8420 (ptm) cc_final: 0.8107 (ptp) REVERT: C 803 GLU cc_start: 0.8930 (mp0) cc_final: 0.8470 (mp0) REVERT: C 806 LEU cc_start: 0.9189 (mt) cc_final: 0.8759 (mt) REVERT: C 819 ARG cc_start: 0.8341 (tmm-80) cc_final: 0.8020 (tmm-80) REVERT: C 1015 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8759 (tp) REVERT: C 1128 MET cc_start: 0.5714 (tpt) cc_final: 0.5370 (tpt) REVERT: D 69 ARG cc_start: 0.8095 (ptm160) cc_final: 0.7793 (ptm160) REVERT: D 81 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 113 ARG cc_start: 0.6949 (ptt180) cc_final: 0.6504 (mmt-90) REVERT: D 256 MET cc_start: 0.7913 (tpp) cc_final: 0.7648 (tpp) REVERT: D 379 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7249 (t0) REVERT: D 670 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7824 (tm-30) REVERT: D 1191 MET cc_start: 0.8729 (pmm) cc_final: 0.8068 (pmm) REVERT: D 1217 THR cc_start: 0.8662 (p) cc_final: 0.8413 (p) REVERT: F 283 LEU cc_start: 0.9282 (mt) cc_final: 0.9047 (mt) REVERT: F 298 MET cc_start: 0.5173 (tpp) cc_final: 0.4919 (tpp) REVERT: F 324 TYR cc_start: 0.8271 (m-80) cc_final: 0.7991 (m-80) REVERT: F 479 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6645 (t80) REVERT: N 79 CYS cc_start: 0.4963 (OUTLIER) cc_final: 0.4501 (m) outliers start: 96 outliers final: 68 residues processed: 381 average time/residue: 0.4031 time to fit residues: 251.9581 Evaluate side-chains 358 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 3.041 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 193 ILE 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 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 246 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 545 VAL 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 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 D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU 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 379 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER 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 541 MET Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 956 THR 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 1131 SER 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 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 434 VAL Chi-restraints excluded: chain F residue 479 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 342 optimal weight: 6.9990 chunk 320 optimal weight: 30.0000 chunk 231 optimal weight: 6.9990 chunk 335 optimal weight: 50.0000 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 140 optimal weight: 0.0970 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** D 752 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.155360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112251 restraints weight = 78216.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112263 restraints weight = 51667.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112966 restraints weight = 45788.093| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31803 Z= 0.170 Angle : 0.667 16.929 43723 Z= 0.339 Chirality : 0.043 0.356 4969 Planarity : 0.004 0.070 5138 Dihedral : 20.926 179.521 5653 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.59 % Allowed : 22.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3513 helix: 1.34 (0.14), residues: 1435 sheet: -0.50 (0.27), residues: 416 loop : -0.55 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 231 HIS 0.005 0.001 HIS C 737 PHE 0.018 0.002 PHE B 63 TYR 0.031 0.001 TYR E 32 ARG 0.009 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 1443) hydrogen bonds : angle 4.22462 ( 3941) metal coordination : bond 0.00727 ( 28) metal coordination : angle 5.66840 ( 24) covalent geometry : bond 0.00395 (31775) covalent geometry : angle 0.65334 (43699) *********************** 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 408 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 302 time to evaluate : 3.340 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: B 78 LEU cc_start: 0.8142 (mp) cc_final: 0.7786 (tt) REVERT: B 152 ASN cc_start: 0.8636 (m-40) cc_final: 0.8326 (p0) REVERT: C 52 ASP cc_start: 0.7332 (p0) cc_final: 0.7022 (p0) REVERT: C 94 THR cc_start: 0.7279 (OUTLIER) cc_final: 0.6902 (p) REVERT: C 442 ASN cc_start: 0.8798 (t0) cc_final: 0.8437 (t0) REVERT: C 460 ASP cc_start: 0.8328 (t0) cc_final: 0.8103 (t0) REVERT: C 499 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: C 517 LEU cc_start: 0.8606 (mp) cc_final: 0.8133 (mp) REVERT: C 648 ASN cc_start: 0.6202 (t0) cc_final: 0.5001 (t0) REVERT: C 710 MET cc_start: 0.8519 (ptm) cc_final: 0.8266 (ptp) REVERT: C 803 GLU cc_start: 0.8847 (mp0) cc_final: 0.8290 (mp0) REVERT: C 806 LEU cc_start: 0.9106 (mt) cc_final: 0.8754 (mt) REVERT: C 819 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.7966 (tmm-80) REVERT: C 1015 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8798 (tp) REVERT: C 1128 MET cc_start: 0.5363 (tpt) cc_final: 0.5050 (tpt) REVERT: D 69 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7795 (ptm160) REVERT: D 113 ARG cc_start: 0.7087 (ptt180) cc_final: 0.6487 (mmt-90) REVERT: D 256 MET cc_start: 0.8104 (tpp) cc_final: 0.7803 (tpp) REVERT: D 379 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7441 (t0) REVERT: D 591 ASP cc_start: 0.8348 (m-30) cc_final: 0.8147 (p0) REVERT: D 670 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 836 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7369 (ttt180) REVERT: D 1006 MET cc_start: 0.1272 (mpp) cc_final: 0.0268 (mmt) REVERT: D 1191 MET cc_start: 0.8616 (pmm) cc_final: 0.8007 (pmm) REVERT: D 1217 THR cc_start: 0.8711 (p) cc_final: 0.8401 (p) REVERT: F 245 PHE cc_start: 0.8033 (m-10) cc_final: 0.7779 (m-10) REVERT: F 283 LEU cc_start: 0.9265 (mt) cc_final: 0.9022 (mt) REVERT: F 298 MET cc_start: 0.5214 (tpp) cc_final: 0.4965 (tpp) REVERT: F 324 TYR cc_start: 0.8103 (m-80) cc_final: 0.7864 (m-80) REVERT: N 79 CYS cc_start: 0.4895 (OUTLIER) cc_final: 0.4465 (m) outliers start: 106 outliers final: 81 residues processed: 385 average time/residue: 0.4237 time to fit residues: 267.5849 Evaluate side-chains 353 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 266 time to evaluate : 3.334 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 100 GLN 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 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 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 246 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 545 VAL 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 759 ILE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 912 MET 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 1056 MET 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 261 LEU 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 379 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 962 CYS Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1116 HIS 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 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 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 348 THR 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 485 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 4 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 15 optimal weight: 0.0060 chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 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 354 HIS ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.154934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.111526 restraints weight = 78764.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109591 restraints weight = 54394.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110607 restraints weight = 53207.882| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31803 Z= 0.180 Angle : 0.686 16.709 43723 Z= 0.349 Chirality : 0.044 0.329 4969 Planarity : 0.005 0.102 5138 Dihedral : 20.903 179.796 5653 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.21 % Allowed : 23.61 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3513 helix: 1.25 (0.14), residues: 1433 sheet: -0.42 (0.27), residues: 401 loop : -0.56 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 231 HIS 0.004 0.001 HIS D 439 PHE 0.036 0.002 PHE A 21 TYR 0.032 0.001 TYR E 32 ARG 0.007 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 1443) hydrogen bonds : angle 4.27715 ( 3941) metal coordination : bond 0.00649 ( 28) metal coordination : angle 5.51248 ( 24) covalent geometry : bond 0.00419 (31775) covalent geometry : angle 0.67425 (43699) *********************** 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 385 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 290 time to evaluate : 3.291 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: 0.7234 (ttm) cc_final: 0.6842 (mtm) REVERT: B 152 ASN cc_start: 0.8785 (m-40) cc_final: 0.8432 (p0) REVERT: C 52 ASP cc_start: 0.7293 (p0) cc_final: 0.7022 (p0) REVERT: C 442 ASN cc_start: 0.8839 (t0) cc_final: 0.8517 (t0) REVERT: C 499 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: C 517 LEU cc_start: 0.8586 (mp) cc_final: 0.8135 (mp) REVERT: C 648 ASN cc_start: 0.6211 (t0) cc_final: 0.4934 (t0) REVERT: C 710 MET cc_start: 0.8511 (ptm) cc_final: 0.8194 (ptp) REVERT: C 803 GLU cc_start: 0.8912 (mp0) cc_final: 0.8308 (mp0) REVERT: C 806 LEU cc_start: 0.9129 (mt) cc_final: 0.8751 (mt) REVERT: C 819 ARG cc_start: 0.8408 (tmm-80) cc_final: 0.8052 (tmm-80) REVERT: C 1015 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8763 (tp) REVERT: C 1128 MET cc_start: 0.5515 (tpt) cc_final: 0.5248 (tpt) REVERT: D 69 ARG cc_start: 0.8197 (ptm160) cc_final: 0.7850 (ptm160) REVERT: D 256 MET cc_start: 0.8100 (tpp) cc_final: 0.7827 (tpp) REVERT: D 296 LEU cc_start: 0.8460 (mt) cc_final: 0.7744 (mt) REVERT: D 379 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7362 (t0) REVERT: D 670 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7860 (tm-30) REVERT: D 809 MET cc_start: 0.7051 (ttt) cc_final: 0.6737 (tmm) REVERT: D 836 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7323 (ttt180) REVERT: D 1006 MET cc_start: 0.1117 (mpp) cc_final: 0.0020 (mmt) REVERT: D 1191 MET cc_start: 0.8626 (pmm) cc_final: 0.8049 (pmm) REVERT: F 245 PHE cc_start: 0.8194 (m-10) cc_final: 0.7973 (m-10) REVERT: F 283 LEU cc_start: 0.9271 (mt) cc_final: 0.9067 (mt) REVERT: F 298 MET cc_start: 0.5484 (tpp) cc_final: 0.5140 (tpp) REVERT: F 324 TYR cc_start: 0.8173 (m-80) cc_final: 0.7824 (m-80) REVERT: N 79 CYS cc_start: 0.5144 (OUTLIER) cc_final: 0.4744 (m) outliers start: 95 outliers final: 79 residues processed: 365 average time/residue: 0.4043 time to fit residues: 244.5911 Evaluate side-chains 353 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 269 time to evaluate : 3.459 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 193 ILE 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 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 304 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 545 VAL 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 759 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 912 MET 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 1056 MET 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 261 LEU 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 379 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 962 CYS Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1116 HIS 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 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 76 ASN Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 349 ILE 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 M residue 52 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 40.0000 chunk 22 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 191 optimal weight: 0.0670 chunk 208 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 301 optimal weight: 0.0030 chunk 288 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 overall best weight: 0.3328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 752 GLN F 252 ASN ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.157312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.115071 restraints weight = 78132.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111801 restraints weight = 59027.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113266 restraints weight = 47976.376| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31803 Z= 0.132 Angle : 0.687 21.648 43723 Z= 0.345 Chirality : 0.043 0.451 4969 Planarity : 0.004 0.049 5138 Dihedral : 20.844 179.288 5653 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.27 % Allowed : 24.73 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3513 helix: 1.29 (0.14), residues: 1433 sheet: -0.41 (0.27), residues: 412 loop : -0.51 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 231 HIS 0.005 0.001 HIS C 462 PHE 0.025 0.001 PHE A 21 TYR 0.026 0.001 TYR E 32 ARG 0.006 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 1443) hydrogen bonds : angle 4.19091 ( 3941) metal coordination : bond 0.00465 ( 28) metal coordination : angle 4.67639 ( 24) covalent geometry : bond 0.00299 (31775) covalent geometry : angle 0.67887 (43699) *********************** 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 386 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 319 time to evaluate : 3.163 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: A 99 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6500 (tppt) REVERT: A 136 MET cc_start: 0.7127 (ttm) cc_final: 0.6794 (mtm) REVERT: B 1 MET cc_start: 0.6998 (mmm) cc_final: 0.6729 (mmm) REVERT: B 38 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7994 (tt) REVERT: B 78 LEU cc_start: 0.8119 (mp) cc_final: 0.7744 (tt) REVERT: B 152 ASN cc_start: 0.8804 (m-40) cc_final: 0.8437 (p0) REVERT: C 52 ASP cc_start: 0.7182 (p0) cc_final: 0.6966 (p0) REVERT: C 94 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7149 (m) REVERT: C 442 ASN cc_start: 0.8762 (t0) cc_final: 0.8392 (t0) REVERT: C 460 ASP cc_start: 0.7897 (t0) cc_final: 0.7653 (m-30) REVERT: C 499 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: C 517 LEU cc_start: 0.8429 (mp) cc_final: 0.7976 (mp) REVERT: C 648 ASN cc_start: 0.6003 (t0) cc_final: 0.4764 (t0) REVERT: C 710 MET cc_start: 0.8451 (ptm) cc_final: 0.8225 (ptp) REVERT: C 803 GLU cc_start: 0.8955 (mp0) cc_final: 0.8327 (mp0) REVERT: C 806 LEU cc_start: 0.9152 (mt) cc_final: 0.8758 (mt) REVERT: C 1015 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8660 (tp) REVERT: C 1128 MET cc_start: 0.5307 (tpt) cc_final: 0.5068 (tpt) REVERT: D 69 ARG cc_start: 0.8238 (ptm160) cc_final: 0.7686 (ptm160) REVERT: D 81 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7340 (tm-30) REVERT: D 344 TYR cc_start: 0.8708 (m-80) cc_final: 0.8080 (m-80) REVERT: D 379 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7231 (t0) REVERT: D 670 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7753 (tm-30) REVERT: D 1006 MET cc_start: 0.1416 (mpp) cc_final: 0.0383 (mmt) REVERT: D 1191 MET cc_start: 0.8712 (pmm) cc_final: 0.8045 (pmm) REVERT: F 245 PHE cc_start: 0.8311 (m-10) cc_final: 0.8048 (m-10) REVERT: F 283 LEU cc_start: 0.9299 (mt) cc_final: 0.9073 (mt) REVERT: F 324 TYR cc_start: 0.8191 (m-80) cc_final: 0.7953 (m-80) outliers start: 67 outliers final: 49 residues processed: 373 average time/residue: 0.4106 time to fit residues: 250.4569 Evaluate side-chains 337 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 3.171 ------------------------------------------------------------------------------- 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 99 LYS 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 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 304 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU 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 908 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1056 MET Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 403 SER 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 819 VAL 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 1053 THR Chi-restraints excluded: chain D residue 1087 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 F residue 233 GLU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain M residue 81 THR 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 179 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 349 optimal weight: 8.9990 chunk 304 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 258 optimal weight: 0.0770 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** 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 = 0.4414 r_free = 0.4414 target = 0.156122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.112915 restraints weight = 78628.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.111299 restraints weight = 52341.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.112241 restraints weight = 51063.599| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31803 Z= 0.151 Angle : 0.700 17.599 43723 Z= 0.351 Chirality : 0.044 0.446 4969 Planarity : 0.004 0.073 5138 Dihedral : 20.836 179.436 5653 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.50 % Allowed : 25.10 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3513 helix: 1.27 (0.14), residues: 1432 sheet: -0.41 (0.27), residues: 412 loop : -0.53 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 231 HIS 0.006 0.001 HIS D1116 PHE 0.032 0.002 PHE D1072 TYR 0.041 0.001 TYR D 867 ARG 0.015 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 1443) hydrogen bonds : angle 4.24775 ( 3941) metal coordination : bond 0.00491 ( 28) metal coordination : angle 4.96264 ( 24) covalent geometry : bond 0.00350 (31775) covalent geometry : angle 0.69057 (43699) ********************** 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 367 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 293 time to evaluate : 3.314 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: A 99 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6519 (tppt) REVERT: A 136 MET cc_start: 0.7157 (ttm) cc_final: 0.6843 (mtm) REVERT: A 151 GLN cc_start: 0.6558 (pp30) cc_final: 0.6083 (pp30) REVERT: B 1 MET cc_start: 0.7115 (mmm) cc_final: 0.6825 (mmm) REVERT: B 152 ASN cc_start: 0.8811 (m-40) cc_final: 0.8487 (p0) REVERT: C 52 ASP cc_start: 0.7146 (p0) cc_final: 0.6934 (p0) REVERT: C 442 ASN cc_start: 0.8825 (t0) cc_final: 0.8444 (t0) REVERT: C 460 ASP cc_start: 0.7970 (t0) cc_final: 0.7695 (m-30) REVERT: C 499 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: C 517 LEU cc_start: 0.8590 (mp) cc_final: 0.8147 (mp) REVERT: C 648 ASN cc_start: 0.5949 (t0) cc_final: 0.4658 (t0) REVERT: C 710 MET cc_start: 0.8457 (ptm) cc_final: 0.8157 (ptp) REVERT: C 803 GLU cc_start: 0.8935 (mp0) cc_final: 0.8328 (mp0) REVERT: C 806 LEU cc_start: 0.9156 (mt) cc_final: 0.8759 (mt) REVERT: C 819 ARG cc_start: 0.8399 (tmm-80) cc_final: 0.8057 (tmm-80) REVERT: C 1015 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8793 (tp) REVERT: C 1128 MET cc_start: 0.5200 (tpt) cc_final: 0.4966 (tpt) REVERT: D 69 ARG cc_start: 0.8267 (ptm160) cc_final: 0.7876 (ptm160) REVERT: D 256 MET cc_start: 0.7858 (tpp) cc_final: 0.7597 (tpp) REVERT: D 344 TYR cc_start: 0.8709 (m-80) cc_final: 0.8060 (m-80) REVERT: D 379 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7352 (t0) REVERT: D 405 MET cc_start: 0.8236 (mtt) cc_final: 0.7731 (mtm) REVERT: D 670 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7836 (tm-30) REVERT: D 809 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6622 (tmt) REVERT: D 836 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7292 (ttt180) REVERT: D 1006 MET cc_start: 0.2234 (mpp) cc_final: 0.1128 (mmt) REVERT: D 1047 ARG cc_start: 0.8140 (mmp-170) cc_final: 0.7913 (mmm160) REVERT: D 1191 MET cc_start: 0.8716 (pmm) cc_final: 0.8050 (pmm) REVERT: F 245 PHE cc_start: 0.8308 (m-10) cc_final: 0.8022 (m-10) REVERT: F 283 LEU cc_start: 0.9281 (mt) cc_final: 0.9069 (mt) REVERT: F 360 ASN cc_start: 0.8933 (p0) cc_final: 0.8696 (p0) REVERT: N 79 CYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4848 (m) outliers start: 74 outliers final: 61 residues processed: 351 average time/residue: 0.4013 time to fit residues: 233.9164 Evaluate side-chains 349 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 3.443 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain A residue 99 LYS 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 93 VAL Chi-restraints excluded: chain B residue 116 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 351 VAL Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 567 VAL 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 759 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1056 MET Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 403 SER 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 809 MET Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 836 ARG 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 1053 THR 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 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 68 LEU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 276 ASN Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain M residue 52 TYR 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 102 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 354 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 349 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 309 optimal weight: 0.0270 chunk 247 optimal weight: 6.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** 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 = 0.156373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113102 restraints weight = 78459.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111533 restraints weight = 51344.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113045 restraints weight = 50211.318| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31803 Z= 0.148 Angle : 0.701 16.089 43723 Z= 0.352 Chirality : 0.044 0.438 4969 Planarity : 0.004 0.072 5138 Dihedral : 20.846 179.062 5653 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.54 % Allowed : 24.93 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3513 helix: 1.34 (0.14), residues: 1424 sheet: -0.36 (0.27), residues: 406 loop : -0.56 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 231 HIS 0.009 0.001 HIS D1116 PHE 0.021 0.002 PHE B 63 TYR 0.026 0.001 TYR E 32 ARG 0.017 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1443) hydrogen bonds : angle 4.21862 ( 3941) metal coordination : bond 0.00460 ( 28) metal coordination : angle 4.77768 ( 24) covalent geometry : bond 0.00343 (31775) covalent geometry : angle 0.69226 (43699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10464.86 seconds wall clock time: 182 minutes 42.58 seconds (10962.58 seconds total)