Starting phenix.real_space_refine on Thu Mar 21 18:33:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpd_32063/03_2024/7vpd_32063.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpd_32063/03_2024/7vpd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpd_32063/03_2024/7vpd_32063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpd_32063/03_2024/7vpd_32063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpd_32063/03_2024/7vpd_32063.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpd_32063/03_2024/7vpd_32063.pdb" } 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 Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 713": "OE1" <-> "OE2" Residue "C GLU 754": "OE1" <-> "OE2" Residue "C GLU 952": "OE1" <-> "OE2" Residue "C GLU 967": "OE1" <-> "OE2" Residue "C GLU 969": "OE1" <-> "OE2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C GLU 1121": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D GLU 745": "OE1" <-> "OE2" Residue "D GLU 749": "OE1" <-> "OE2" Residue "D GLU 837": "OE1" <-> "OE2" Residue "D GLU 999": "OE1" <-> "OE2" Residue "D GLU 1028": "OE1" <-> "OE2" Residue "D GLU 1031": "OE1" <-> "OE2" Residue "D GLU 1120": "OE1" <-> "OE2" Residue "D GLU 1211": "OE1" <-> "OE2" Residue "D GLU 1256": "OE1" <-> "OE2" Residue "D GLU 1260": "OE1" <-> "OE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "F GLU 380": "OE1" <-> "OE2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F ASP 415": "OD1" <-> "OD2" Residue "F GLU 423": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.10, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 14.40 Conformation dependent library (CDL) restraints added in 5.6 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: 10.94 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: 16.17 Time building geometry restraints manager: 15.24 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: 98.15 - 105.34: 1199 105.34 - 112.53: 16565 112.53 - 119.72: 11195 119.72 - 126.91: 14057 126.91 - 134.10: 683 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 2.520 ... (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 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: 2.600 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: 13.030 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 98.800 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.400 ------------------------------------------------------------------------------- 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 31775 Z= 0.297 Angle : 0.792 9.662 43699 Z= 0.446 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 *********************** 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 fitting. rotamer outliers: 13 poor density : 391 time to evaluate : 3.405 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: 0.4729 time to fit residues: 289.3725 Evaluate side-chains 316 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 312 time to evaluate : 3.359 ------------------------------------------------------------------------------- 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: 4.9990 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 331 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN B 185 GLN ** C 235 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 440 GLN D1210 GLN E 64 HIS F 305 GLN F 468 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31775 Z= 0.302 Angle : 0.682 11.426 43699 Z= 0.362 Chirality : 0.044 0.219 4969 Planarity : 0.005 0.060 5138 Dihedral : 21.120 179.053 5659 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.76 % Allowed : 19.05 % Favored : 77.20 % 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: 0.09 (0.14), residues: 3513 helix: 1.19 (0.14), residues: 1433 sheet: -0.69 (0.26), residues: 386 loop : -0.69 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 718 HIS 0.007 0.001 HIS F 499 PHE 0.022 0.002 PHE D 226 TYR 0.037 0.002 TYR E 32 ARG 0.013 0.001 ARG B 182 *********************** 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 465 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 354 time to evaluate : 3.516 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: B 78 LEU cc_start: 0.8188 (mp) cc_final: 0.7949 (tt) REVERT: C 55 LYS cc_start: 0.8763 (ptpt) cc_final: 0.8525 (ptpp) REVERT: C 94 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6714 (p) REVERT: C 109 GLU cc_start: 0.7047 (tp30) cc_final: 0.6713 (tp30) REVERT: C 442 ASN cc_start: 0.8919 (t0) cc_final: 0.8697 (t0) REVERT: C 517 LEU cc_start: 0.8229 (mp) cc_final: 0.7705 (mp) REVERT: C 579 MET cc_start: 0.8656 (mmp) cc_final: 0.8235 (mmp) REVERT: C 648 ASN cc_start: 0.5341 (t0) cc_final: 0.4467 (t0) REVERT: C 710 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8290 (ptp) REVERT: C 749 LYS cc_start: 0.8746 (tppt) cc_final: 0.8418 (ttmt) REVERT: C 759 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8759 (tp) REVERT: C 803 GLU cc_start: 0.8920 (mp0) cc_final: 0.8589 (mp0) REVERT: C 969 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5708 (mm-30) REVERT: D 43 LYS cc_start: 0.7814 (tppt) cc_final: 0.7613 (mptt) REVERT: D 70 PHE cc_start: 0.8219 (p90) cc_final: 0.7739 (p90) REVERT: D 113 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7047 (ptt180) REVERT: D 296 LEU cc_start: 0.8486 (mt) cc_final: 0.8038 (mt) REVERT: D 312 MET cc_start: 0.8713 (mmt) cc_final: 0.8496 (mmm) REVERT: D 861 ARG cc_start: 0.6182 (mmm160) cc_final: 0.5897 (mtp180) REVERT: D 1236 ILE cc_start: 0.8504 (mm) cc_final: 0.8192 (mt) REVERT: F 233 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: F 245 PHE cc_start: 0.8324 (m-10) cc_final: 0.8015 (m-10) REVERT: F 276 ASN cc_start: 0.8981 (m110) cc_final: 0.8774 (p0) REVERT: F 279 LEU cc_start: 0.8994 (mt) cc_final: 0.8749 (pp) REVERT: F 283 LEU cc_start: 0.9233 (mt) cc_final: 0.9003 (mt) REVERT: F 360 ASN cc_start: 0.9165 (p0) cc_final: 0.8882 (p0) REVERT: F 479 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7340 (t80) REVERT: F 494 MET cc_start: 0.9178 (ptt) cc_final: 0.8965 (ptt) REVERT: N 79 CYS cc_start: 0.5000 (OUTLIER) cc_final: 0.3402 (m) outliers start: 111 outliers final: 56 residues processed: 425 average time/residue: 0.4450 time to fit residues: 303.6872 Evaluate side-chains 369 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 305 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 614 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 867 ASP 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 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 873 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1116 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 311 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 332 optimal weight: 50.0000 chunk 358 optimal weight: 40.0000 chunk 295 optimal weight: 0.8980 chunk 329 optimal weight: 30.0000 chunk 113 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN C 529 GLN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31775 Z= 0.249 Angle : 0.631 12.750 43699 Z= 0.334 Chirality : 0.043 0.348 4969 Planarity : 0.004 0.058 5138 Dihedral : 21.054 179.951 5656 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.82 % Allowed : 20.67 % Favored : 75.51 % 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: 1.28 (0.14), residues: 1437 sheet: -0.57 (0.26), residues: 374 loop : -0.64 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 718 HIS 0.006 0.001 HIS F 499 PHE 0.026 0.002 PHE A 21 TYR 0.033 0.001 TYR E 32 ARG 0.005 0.000 ARG C 384 *********************** 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 447 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 334 time to evaluate : 3.637 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: A 213 LYS cc_start: 0.9197 (tptp) cc_final: 0.8897 (tmtt) REVERT: B 78 LEU cc_start: 0.8154 (mp) cc_final: 0.7840 (tt) REVERT: C 94 THR cc_start: 0.7110 (OUTLIER) cc_final: 0.6803 (p) REVERT: C 442 ASN cc_start: 0.8939 (t0) cc_final: 0.8688 (t0) REVERT: C 517 LEU cc_start: 0.8299 (mp) cc_final: 0.7777 (mp) REVERT: C 648 ASN cc_start: 0.5207 (t0) cc_final: 0.4474 (t0) REVERT: C 710 MET cc_start: 0.8510 (ptm) cc_final: 0.8244 (ptp) REVERT: C 749 LYS cc_start: 0.8726 (tppt) cc_final: 0.8419 (ttmt) REVERT: C 803 GLU cc_start: 0.9018 (mp0) cc_final: 0.8670 (mp0) REVERT: C 819 ARG cc_start: 0.8084 (tmm-80) cc_final: 0.7480 (tmm-80) REVERT: C 900 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: D 43 LYS cc_start: 0.7854 (tppt) cc_final: 0.7636 (mptt) REVERT: D 81 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7310 (tm-30) REVERT: D 135 MET cc_start: 0.7476 (mtp) cc_final: 0.7251 (mtt) REVERT: D 312 MET cc_start: 0.8748 (mmt) cc_final: 0.8503 (mmm) REVERT: D 475 MET cc_start: 0.7441 (ttm) cc_final: 0.7200 (ttt) REVERT: D 612 MET cc_start: 0.8956 (ttt) cc_final: 0.8707 (ttt) REVERT: D 836 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7100 (ttt90) REVERT: D 874 ASP cc_start: 0.7785 (t0) cc_final: 0.7509 (t0) REVERT: D 1006 MET cc_start: 0.1686 (mtm) cc_final: 0.0737 (mmt) REVERT: D 1209 PHE cc_start: 0.8366 (t80) cc_final: 0.8033 (t80) REVERT: D 1236 ILE cc_start: 0.8556 (mm) cc_final: 0.8293 (mt) REVERT: F 233 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: F 245 PHE cc_start: 0.8470 (m-10) cc_final: 0.8048 (m-10) REVERT: F 283 LEU cc_start: 0.9222 (mt) cc_final: 0.8994 (mt) REVERT: F 360 ASN cc_start: 0.9135 (p0) cc_final: 0.8856 (p0) REVERT: F 479 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.7375 (t80) REVERT: N 79 CYS cc_start: 0.5357 (OUTLIER) cc_final: 0.3884 (m) outliers start: 113 outliers final: 62 residues processed: 417 average time/residue: 0.4492 time to fit residues: 300.5119 Evaluate side-chains 362 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 3.309 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 ASN 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 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 614 THR 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 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 900 ASP 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 1015 ILE Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain C residue 1116 LEU 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 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain 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 311 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 479 TYR 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 328 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 158 optimal weight: 0.3980 chunk 222 optimal weight: 0.7980 chunk 333 optimal weight: 20.0000 chunk 352 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 315 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31775 Z= 0.283 Angle : 0.647 11.127 43699 Z= 0.339 Chirality : 0.043 0.377 4969 Planarity : 0.004 0.054 5138 Dihedral : 21.030 179.566 5656 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.30 % Allowed : 21.85 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.14), residues: 3513 helix: 1.23 (0.14), residues: 1443 sheet: -0.51 (0.27), residues: 376 loop : -0.65 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 718 HIS 0.007 0.001 HIS F 499 PHE 0.022 0.002 PHE D 248 TYR 0.035 0.001 TYR E 32 ARG 0.006 0.000 ARG B 182 *********************** 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 441 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 314 time to evaluate : 2.770 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 213 LYS cc_start: 0.9235 (tptp) cc_final: 0.8975 (tmtt) REVERT: B 78 LEU cc_start: 0.8234 (mp) cc_final: 0.7979 (mt) REVERT: C 94 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6917 (p) REVERT: C 398 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7182 (mt) REVERT: C 442 ASN cc_start: 0.8941 (t0) cc_final: 0.8686 (t0) REVERT: C 517 LEU cc_start: 0.8398 (mp) cc_final: 0.7908 (mp) REVERT: C 648 ASN cc_start: 0.5374 (t0) cc_final: 0.4664 (t0) REVERT: C 710 MET cc_start: 0.8502 (ptm) cc_final: 0.8256 (ptp) REVERT: C 803 GLU cc_start: 0.9017 (mp0) cc_final: 0.8576 (mp0) REVERT: C 806 LEU cc_start: 0.9086 (mt) cc_final: 0.8740 (mt) REVERT: C 819 ARG cc_start: 0.8082 (tmm-80) cc_final: 0.7581 (tmm-80) REVERT: C 900 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: D 69 ARG cc_start: 0.8471 (ptm160) cc_final: 0.8153 (ptm160) REVERT: D 242 ARG cc_start: 0.8648 (ptp-110) cc_final: 0.8225 (ptp-170) REVERT: D 256 MET cc_start: 0.7871 (tpp) cc_final: 0.7619 (tpp) REVERT: D 330 LEU cc_start: 0.8483 (tp) cc_final: 0.8272 (tt) REVERT: D 405 MET cc_start: 0.8134 (mtt) cc_final: 0.7812 (mtt) REVERT: D 836 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7193 (ttt90) REVERT: D 1006 MET cc_start: 0.1690 (mtm) cc_final: 0.1228 (mmt) REVERT: D 1191 MET cc_start: 0.8808 (pmm) cc_final: 0.8187 (pmm) REVERT: D 1209 PHE cc_start: 0.8459 (t80) cc_final: 0.8253 (t80) REVERT: F 233 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: F 245 PHE cc_start: 0.8561 (m-10) cc_final: 0.8078 (m-10) REVERT: F 283 LEU cc_start: 0.9239 (mt) cc_final: 0.9016 (mt) REVERT: F 479 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7365 (t80) REVERT: N 50 THR cc_start: -0.4777 (OUTLIER) cc_final: -0.5077 (t) REVERT: N 79 CYS cc_start: 0.5399 (OUTLIER) cc_final: 0.3883 (m) outliers start: 127 outliers final: 88 residues processed: 415 average time/residue: 0.3981 time to fit residues: 268.9070 Evaluate side-chains 382 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 286 time to evaluate : 3.694 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain B residue 1 MET 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 109 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 120 ASN 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 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 614 THR 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 668 THR Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 60 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 319 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 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 627 ILE Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 873 VAL Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 17 ASP 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 311 LEU 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 464 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 8.9990 chunk 200 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 262 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 316 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 HIS ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31775 Z= 0.286 Angle : 0.648 11.781 43699 Z= 0.339 Chirality : 0.043 0.371 4969 Planarity : 0.004 0.054 5138 Dihedral : 21.007 178.367 5656 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.91 % Allowed : 22.29 % Favored : 72.80 % 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: 0.15 (0.14), residues: 3513 helix: 1.20 (0.14), residues: 1447 sheet: -0.65 (0.27), residues: 394 loop : -0.64 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 231 HIS 0.006 0.001 HIS F 499 PHE 0.017 0.002 PHE D 248 TYR 0.035 0.002 TYR E 32 ARG 0.009 0.000 ARG D 757 *********************** 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 455 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 310 time to evaluate : 3.608 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: B 78 LEU cc_start: 0.8269 (mp) cc_final: 0.8021 (mt) REVERT: C 94 THR cc_start: 0.7275 (OUTLIER) cc_final: 0.6904 (p) REVERT: C 359 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6323 (t80) REVERT: C 398 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7183 (mt) REVERT: C 442 ASN cc_start: 0.8961 (t0) cc_final: 0.8714 (t0) REVERT: C 517 LEU cc_start: 0.8436 (mp) cc_final: 0.7921 (mp) REVERT: C 648 ASN cc_start: 0.5180 (t0) cc_final: 0.4470 (t0) REVERT: C 710 MET cc_start: 0.8487 (ptm) cc_final: 0.8271 (ptp) REVERT: C 803 GLU cc_start: 0.8991 (mp0) cc_final: 0.8495 (mp0) REVERT: C 806 LEU cc_start: 0.9202 (mt) cc_final: 0.8806 (mt) REVERT: C 819 ARG cc_start: 0.8095 (tmm-80) cc_final: 0.7670 (tmm-80) REVERT: D 69 ARG cc_start: 0.8561 (ptm160) cc_final: 0.8175 (ptm160) REVERT: D 242 ARG cc_start: 0.8633 (ptp-110) cc_final: 0.8212 (ptp-170) REVERT: D 256 MET cc_start: 0.8005 (tpp) cc_final: 0.7699 (tpp) REVERT: D 330 LEU cc_start: 0.8600 (tp) cc_final: 0.8309 (tt) REVERT: D 836 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7364 (ttt90) REVERT: D 1191 MET cc_start: 0.8752 (pmm) cc_final: 0.8245 (pmm) REVERT: F 245 PHE cc_start: 0.8633 (m-10) cc_final: 0.8121 (m-10) REVERT: F 283 LEU cc_start: 0.9247 (mt) cc_final: 0.9029 (mt) REVERT: F 324 TYR cc_start: 0.8369 (m-80) cc_final: 0.8068 (m-80) REVERT: F 479 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7301 (t80) REVERT: N 50 THR cc_start: -0.4615 (OUTLIER) cc_final: -0.4898 (t) REVERT: N 79 CYS cc_start: 0.5460 (OUTLIER) cc_final: 0.3913 (m) outliers start: 145 outliers final: 107 residues processed: 428 average time/residue: 0.4057 time to fit residues: 283.5088 Evaluate side-chains 399 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 285 time to evaluate : 3.428 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 206 ASP 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 87 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 880 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 1072 GLU Chi-restraints excluded: chain C residue 1078 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 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 627 ILE Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 827 ILE 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 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1065 ASP 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 E residue 17 ASP 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 E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 393 VAL 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 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 10.0000 chunk 317 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 207 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN D 416 ASN ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31775 Z= 0.198 Angle : 0.621 11.463 43699 Z= 0.322 Chirality : 0.042 0.272 4969 Planarity : 0.004 0.077 5138 Dihedral : 20.971 179.067 5653 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 24.32 % Favored : 72.16 % 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: 1.40 (0.14), residues: 1428 sheet: -0.50 (0.27), residues: 397 loop : -0.61 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 231 HIS 0.008 0.001 HIS E 64 PHE 0.030 0.001 PHE D 226 TYR 0.029 0.001 TYR E 32 ARG 0.007 0.000 ARG C 544 *********************** 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 423 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 319 time to evaluate : 3.171 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: C 398 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7042 (mt) REVERT: C 401 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7627 (tp40) REVERT: C 442 ASN cc_start: 0.8933 (t0) cc_final: 0.8659 (t0) REVERT: C 499 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: C 517 LEU cc_start: 0.8300 (mp) cc_final: 0.7765 (mp) REVERT: C 648 ASN cc_start: 0.5028 (t0) cc_final: 0.4377 (t0) REVERT: C 710 MET cc_start: 0.8499 (ptm) cc_final: 0.8297 (ptp) REVERT: C 749 LYS cc_start: 0.8861 (tptt) cc_final: 0.8472 (mttt) REVERT: C 803 GLU cc_start: 0.8989 (mp0) cc_final: 0.8486 (mp0) REVERT: C 806 LEU cc_start: 0.9242 (mt) cc_final: 0.8806 (mt) REVERT: C 969 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5584 (mm-30) REVERT: C 1015 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8622 (tp) REVERT: C 1128 MET cc_start: 0.4992 (tpt) cc_final: 0.4600 (tpt) REVERT: D 69 ARG cc_start: 0.8478 (ptm160) cc_final: 0.8012 (ptm160) REVERT: D 81 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7260 (tm-30) REVERT: D 242 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.8285 (ptp-170) REVERT: D 256 MET cc_start: 0.7962 (tpp) cc_final: 0.7717 (tpp) REVERT: D 330 LEU cc_start: 0.8555 (tp) cc_final: 0.8273 (tt) REVERT: D 344 TYR cc_start: 0.8817 (m-80) cc_final: 0.8114 (m-80) REVERT: D 405 MET cc_start: 0.8120 (mtt) cc_final: 0.7874 (mtt) REVERT: D 828 PRO cc_start: 0.8811 (Cg_endo) cc_final: 0.8589 (Cg_exo) REVERT: D 836 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7281 (ttt90) REVERT: D 1006 MET cc_start: 0.1238 (mtm) cc_final: 0.0406 (mmt) REVERT: D 1191 MET cc_start: 0.8803 (pmm) cc_final: 0.8240 (pmm) REVERT: F 245 PHE cc_start: 0.8633 (m-10) cc_final: 0.8139 (m-10) REVERT: F 283 LEU cc_start: 0.9229 (mt) cc_final: 0.9018 (mt) REVERT: F 298 MET cc_start: 0.5461 (tpp) cc_final: 0.5103 (tpp) REVERT: F 324 TYR cc_start: 0.8333 (m-80) cc_final: 0.8017 (m-80) REVERT: F 479 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7194 (t80) REVERT: N 50 THR cc_start: -0.4532 (OUTLIER) cc_final: -0.4834 (t) REVERT: N 79 CYS cc_start: 0.5173 (OUTLIER) cc_final: 0.3573 (m) outliers start: 104 outliers final: 78 residues processed: 397 average time/residue: 0.4123 time to fit residues: 266.7162 Evaluate side-chains 381 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 295 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL 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 A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ASN 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 156 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 499 GLU 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 859 VAL Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 969 GLU 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 1072 GLU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 503 THR 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 792 ASN Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 827 ILE 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 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1059 ILE 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 17 ASP 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 233 GLU Chi-restraints excluded: chain F residue 311 LEU 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 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 50.0000 chunk 39 optimal weight: 0.3980 chunk 201 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS F 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31775 Z= 0.233 Angle : 0.637 12.462 43699 Z= 0.329 Chirality : 0.042 0.396 4969 Planarity : 0.004 0.049 5138 Dihedral : 20.944 179.314 5651 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.16 % Allowed : 23.85 % Favored : 71.99 % 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: 0.31 (0.14), residues: 3513 helix: 1.39 (0.14), residues: 1437 sheet: -0.54 (0.27), residues: 392 loop : -0.61 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 231 HIS 0.007 0.001 HIS D1133 PHE 0.023 0.001 PHE D1209 TYR 0.031 0.001 TYR E 32 ARG 0.009 0.000 ARG D1047 *********************** 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 431 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 308 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6891 (ttm) cc_final: 0.6504 (mtm) REVERT: C 398 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.7052 (mt) REVERT: C 442 ASN cc_start: 0.8947 (t0) cc_final: 0.8672 (t0) REVERT: C 499 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: C 517 LEU cc_start: 0.8404 (mp) cc_final: 0.7881 (mp) REVERT: C 648 ASN cc_start: 0.5179 (t0) cc_final: 0.4501 (t0) REVERT: C 749 LYS cc_start: 0.8839 (tptt) cc_final: 0.8543 (mttt) REVERT: C 803 GLU cc_start: 0.8994 (mp0) cc_final: 0.8487 (mp0) REVERT: C 806 LEU cc_start: 0.9195 (mt) cc_final: 0.8846 (mt) REVERT: C 1015 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8605 (tp) REVERT: C 1073 LEU cc_start: 0.9207 (mm) cc_final: 0.8962 (mm) REVERT: C 1128 MET cc_start: 0.5035 (tpt) cc_final: 0.4696 (tpt) REVERT: D 69 ARG cc_start: 0.8522 (ptm160) cc_final: 0.8181 (ptm160) REVERT: D 81 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7244 (tm-30) REVERT: D 256 MET cc_start: 0.8000 (tpp) cc_final: 0.7691 (tpp) REVERT: D 405 MET cc_start: 0.8146 (mtt) cc_final: 0.7893 (mtt) REVERT: D 836 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7373 (ttt90) REVERT: D 1047 ARG cc_start: 0.8584 (mmp-170) cc_final: 0.8095 (mmm160) REVERT: D 1191 MET cc_start: 0.8744 (pmm) cc_final: 0.8258 (pmm) REVERT: F 245 PHE cc_start: 0.8648 (m-10) cc_final: 0.8405 (m-10) REVERT: F 298 MET cc_start: 0.5419 (tpp) cc_final: 0.5055 (tpp) REVERT: F 324 TYR cc_start: 0.8248 (m-80) cc_final: 0.7930 (m-80) REVERT: F 479 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7148 (t80) REVERT: N 50 THR cc_start: -0.4397 (OUTLIER) cc_final: -0.4684 (t) REVERT: N 79 CYS cc_start: 0.5223 (OUTLIER) cc_final: 0.3600 (m) outliers start: 123 outliers final: 98 residues processed: 403 average time/residue: 0.4561 time to fit residues: 299.0293 Evaluate side-chains 398 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 293 time to evaluate : 3.482 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 152 ASN 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 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 72 SER 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 292 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 614 THR 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 724 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 867 ASP 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 1036 MET Chi-restraints excluded: chain C residue 1056 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 807 MET 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 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 17 ASP 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 E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 311 LEU 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 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 82 GLN ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31775 Z= 0.222 Angle : 0.648 20.091 43699 Z= 0.331 Chirality : 0.042 0.310 4969 Planarity : 0.004 0.088 5138 Dihedral : 20.925 179.739 5651 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.30 % Allowed : 23.92 % Favored : 71.79 % 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: 0.34 (0.14), residues: 3513 helix: 1.41 (0.14), residues: 1438 sheet: -0.53 (0.27), residues: 392 loop : -0.59 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 199 HIS 0.007 0.001 HIS E 64 PHE 0.019 0.001 PHE C 141 TYR 0.030 0.001 TYR E 32 ARG 0.008 0.000 ARG D1047 *********************** 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 428 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 301 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.6841 (OUTLIER) cc_final: 0.6464 (tppt) REVERT: A 136 MET cc_start: 0.6832 (ttm) cc_final: 0.6438 (mtm) REVERT: C 285 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8324 (mt-10) REVERT: C 359 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6178 (t80) REVERT: C 398 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6939 (mt) REVERT: C 442 ASN cc_start: 0.8943 (t0) cc_final: 0.8648 (t0) REVERT: C 499 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: C 517 LEU cc_start: 0.8365 (mp) cc_final: 0.7852 (mp) REVERT: C 648 ASN cc_start: 0.5157 (t0) cc_final: 0.4478 (t0) REVERT: C 749 LYS cc_start: 0.8850 (tptt) cc_final: 0.8583 (mttt) REVERT: C 803 GLU cc_start: 0.8987 (mp0) cc_final: 0.8485 (mp0) REVERT: C 806 LEU cc_start: 0.9209 (mt) cc_final: 0.8842 (mt) REVERT: C 1015 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8583 (tp) REVERT: C 1073 LEU cc_start: 0.9136 (mm) cc_final: 0.8862 (mm) REVERT: C 1128 MET cc_start: 0.5113 (tpt) cc_final: 0.4802 (tpt) REVERT: D 69 ARG cc_start: 0.8519 (ptm160) cc_final: 0.8106 (ptm160) REVERT: D 81 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7246 (tm-30) REVERT: D 256 MET cc_start: 0.8008 (tpp) cc_final: 0.7687 (tpp) REVERT: D 344 TYR cc_start: 0.8834 (m-80) cc_final: 0.8131 (m-80) REVERT: D 405 MET cc_start: 0.8139 (mtt) cc_final: 0.7901 (mtt) REVERT: D 836 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7361 (ttt90) REVERT: D 1047 ARG cc_start: 0.8604 (mmp-170) cc_final: 0.8134 (mmm160) REVERT: D 1191 MET cc_start: 0.8685 (pmm) cc_final: 0.8202 (pmm) REVERT: F 245 PHE cc_start: 0.8668 (m-10) cc_final: 0.8424 (m-10) REVERT: F 298 MET cc_start: 0.5425 (tpp) cc_final: 0.5199 (tpp) REVERT: F 324 TYR cc_start: 0.8181 (m-80) cc_final: 0.7841 (m-80) REVERT: F 418 PHE cc_start: 0.8194 (t80) cc_final: 0.7989 (t80) REVERT: F 479 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7153 (t80) REVERT: N 50 THR cc_start: -0.4422 (OUTLIER) cc_final: -0.4709 (t) REVERT: N 79 CYS cc_start: 0.5233 (OUTLIER) cc_final: 0.3633 (m) outliers start: 127 outliers final: 103 residues processed: 402 average time/residue: 0.4535 time to fit residues: 297.1636 Evaluate side-chains 402 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 290 time to evaluate : 3.423 ------------------------------------------------------------------------------- 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 99 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASN 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 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 614 THR 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 724 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 867 ASP 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 1036 MET Chi-restraints excluded: chain C residue 1056 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1078 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 807 MET 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 956 THR Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 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 17 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 10.0000 chunk 337 optimal weight: 50.0000 chunk 307 optimal weight: 0.5980 chunk 327 optimal weight: 8.9990 chunk 336 optimal weight: 50.0000 chunk 197 optimal weight: 0.2980 chunk 142 optimal weight: 0.0370 chunk 257 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 296 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- 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 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31775 Z= 0.254 Angle : 0.658 16.985 43699 Z= 0.337 Chirality : 0.043 0.291 4969 Planarity : 0.004 0.068 5138 Dihedral : 20.886 179.966 5651 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.06 % Allowed : 24.29 % Favored : 71.65 % 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: 1.36 (0.14), residues: 1440 sheet: -0.54 (0.27), residues: 400 loop : -0.60 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 199 HIS 0.007 0.001 HIS D1133 PHE 0.020 0.001 PHE D1072 TYR 0.031 0.001 TYR E 32 ARG 0.007 0.000 ARG D1047 *********************** 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 420 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 300 time to evaluate : 2.900 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 99 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6466 (tppt) REVERT: C 285 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 359 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6258 (t80) REVERT: C 398 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6944 (mt) REVERT: C 442 ASN cc_start: 0.8989 (t0) cc_final: 0.8732 (t0) REVERT: C 460 ASP cc_start: 0.8141 (t0) cc_final: 0.7869 (m-30) REVERT: C 499 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: C 517 LEU cc_start: 0.8430 (mp) cc_final: 0.7921 (mp) REVERT: C 648 ASN cc_start: 0.5196 (t0) cc_final: 0.4478 (t0) REVERT: C 749 LYS cc_start: 0.8882 (tptt) cc_final: 0.8545 (mttt) REVERT: C 803 GLU cc_start: 0.8983 (mp0) cc_final: 0.8472 (mp0) REVERT: C 806 LEU cc_start: 0.9176 (mt) cc_final: 0.8785 (mt) REVERT: C 1015 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8590 (tp) REVERT: C 1073 LEU cc_start: 0.9181 (mm) cc_final: 0.8911 (mm) REVERT: C 1128 MET cc_start: 0.4733 (tpt) cc_final: 0.4442 (tpt) REVERT: D 69 ARG cc_start: 0.8555 (ptm160) cc_final: 0.8139 (ptm160) REVERT: D 405 MET cc_start: 0.8137 (mtt) cc_final: 0.7836 (mtt) REVERT: D 836 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7309 (ttt90) REVERT: D 1006 MET cc_start: 0.1218 (mpp) cc_final: 0.0270 (mmt) REVERT: D 1047 ARG cc_start: 0.8619 (mmp-170) cc_final: 0.8153 (mmm160) REVERT: D 1191 MET cc_start: 0.8691 (pmm) cc_final: 0.8238 (pmm) REVERT: F 245 PHE cc_start: 0.8616 (m-10) cc_final: 0.8368 (m-10) REVERT: F 298 MET cc_start: 0.5565 (tpp) cc_final: 0.5329 (tpp) REVERT: F 324 TYR cc_start: 0.8181 (m-80) cc_final: 0.7962 (m-80) REVERT: F 479 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7156 (t80) REVERT: N 50 THR cc_start: -0.4483 (OUTLIER) cc_final: -0.4775 (t) REVERT: N 79 CYS cc_start: 0.5265 (OUTLIER) cc_final: 0.3691 (m) outliers start: 120 outliers final: 107 residues processed: 395 average time/residue: 0.4071 time to fit residues: 261.0414 Evaluate side-chains 399 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 283 time to evaluate : 3.377 ------------------------------------------------------------------------------- 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 99 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASN 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 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 72 SER 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 176 ASP Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 614 THR 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 673 LYS Chi-restraints excluded: chain C residue 724 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 867 ASP 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 1036 MET Chi-restraints excluded: chain C residue 1056 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1078 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 807 MET 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 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1065 ASP 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 17 ASP 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 276 ASN Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 30.0000 chunk 215 optimal weight: 1.9990 chunk 346 optimal weight: 30.0000 chunk 211 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 240 optimal weight: 0.6980 chunk 363 optimal weight: 40.0000 chunk 334 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 223 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31775 Z= 0.232 Angle : 0.663 17.849 43699 Z= 0.338 Chirality : 0.043 0.272 4969 Planarity : 0.004 0.057 5138 Dihedral : 20.866 179.613 5651 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.03 % Allowed : 24.29 % Favored : 71.68 % 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: 1.34 (0.14), residues: 1439 sheet: -0.49 (0.27), residues: 401 loop : -0.63 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 199 HIS 0.006 0.001 HIS D1133 PHE 0.025 0.001 PHE D 226 TYR 0.030 0.001 TYR E 32 ARG 0.013 0.000 ARG D 276 ********************** 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 411 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 292 time to evaluate : 3.154 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 99 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6459 (tppt) REVERT: C 359 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6262 (t80) REVERT: C 398 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6868 (mt) REVERT: C 442 ASN cc_start: 0.8983 (t0) cc_final: 0.8722 (t0) REVERT: C 499 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: C 517 LEU cc_start: 0.8422 (mp) cc_final: 0.7926 (mp) REVERT: C 648 ASN cc_start: 0.5199 (t0) cc_final: 0.4482 (t0) REVERT: C 749 LYS cc_start: 0.8856 (tptt) cc_final: 0.8525 (mttt) REVERT: C 803 GLU cc_start: 0.8975 (mp0) cc_final: 0.8465 (mp0) REVERT: C 806 LEU cc_start: 0.9199 (mt) cc_final: 0.8805 (mt) REVERT: C 1015 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8583 (tp) REVERT: C 1073 LEU cc_start: 0.9185 (mm) cc_final: 0.8916 (mm) REVERT: C 1128 MET cc_start: 0.4745 (tpt) cc_final: 0.4491 (tpt) REVERT: D 69 ARG cc_start: 0.8593 (ptm160) cc_final: 0.8185 (ptm160) REVERT: D 256 MET cc_start: 0.7935 (tpp) cc_final: 0.7623 (tpp) REVERT: D 344 TYR cc_start: 0.8807 (m-80) cc_final: 0.8021 (m-80) REVERT: D 405 MET cc_start: 0.8144 (mtt) cc_final: 0.7893 (mtt) REVERT: D 836 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7276 (ttt90) REVERT: D 1006 MET cc_start: 0.1284 (mpp) cc_final: 0.0240 (mmt) REVERT: D 1047 ARG cc_start: 0.8627 (mmp-170) cc_final: 0.8393 (mmp-170) REVERT: D 1191 MET cc_start: 0.8693 (pmm) cc_final: 0.8229 (pmm) REVERT: F 245 PHE cc_start: 0.8606 (m-10) cc_final: 0.8345 (m-10) REVERT: F 298 MET cc_start: 0.5559 (tpp) cc_final: 0.5324 (tpp) REVERT: F 479 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7070 (t80) REVERT: N 50 THR cc_start: -0.4420 (OUTLIER) cc_final: -0.4824 (t) outliers start: 119 outliers final: 107 residues processed: 387 average time/residue: 0.4086 time to fit residues: 258.5871 Evaluate side-chains 399 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 284 time to evaluate : 3.356 ------------------------------------------------------------------------------- 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 99 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASN 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 87 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 72 SER 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 176 ASP Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 614 THR 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 673 LYS Chi-restraints excluded: chain C residue 724 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 867 ASP 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 1036 MET Chi-restraints excluded: chain C residue 1056 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1078 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 102 THR 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 320 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 669 ASN Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS 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 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1065 ASP 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 17 ASP 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 276 ASN Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 50 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 177 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 chunk 88 optimal weight: 0.0070 chunk 266 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.154851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.112462 restraints weight = 78279.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108601 restraints weight = 61998.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.110057 restraints weight = 51706.110| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31775 Z= 0.216 Angle : 0.654 17.449 43699 Z= 0.335 Chirality : 0.042 0.257 4969 Planarity : 0.004 0.059 5138 Dihedral : 20.862 179.904 5651 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.89 % Allowed : 24.63 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.14), residues: 1439 sheet: -0.50 (0.27), residues: 410 loop : -0.61 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 199 HIS 0.005 0.001 HIS D1116 PHE 0.034 0.001 PHE D1209 TYR 0.029 0.001 TYR E 32 ARG 0.009 0.000 ARG C 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.76 seconds wall clock time: 116 minutes 6.93 seconds (6966.93 seconds total)