Starting phenix.real_space_refine on Sun Apr 14 01:16:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py5_13713/04_2024/7py5_13713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py5_13713/04_2024/7py5_13713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py5_13713/04_2024/7py5_13713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py5_13713/04_2024/7py5_13713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py5_13713/04_2024/7py5_13713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py5_13713/04_2024/7py5_13713.pdb" } resolution = 3.9 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= 0.009 sd= 0.079 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 2 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 18481 2.51 5 N 5372 2.21 5 O 5923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 76": "OE1" <-> "OE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C ASP 1297": "OD1" <-> "OD2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 699": "OD1" <-> "OD2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1254": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29959 Number of models: 1 Model: "" Number of chains: 11 Chain: "N" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 987 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 42, 'PHE:plan': 14, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 830 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15888 SG CYS D 72 89.630 117.509 74.292 1.00 87.14 S ATOM 16020 SG CYS D 88 90.353 114.489 71.900 1.00 79.51 S ATOM 21708 SG CYS D 814 97.803 46.850 77.435 1.00 54.18 S ATOM 22273 SG CYS D 888 99.725 50.068 76.747 1.00 43.10 S ATOM 22324 SG CYS D 895 98.532 49.462 80.225 1.00 39.84 S ATOM 22345 SG CYS D 898 101.236 47.214 78.869 1.00 41.30 S Time building chain proxies: 17.37, per 1000 atoms: 0.58 Number of scatterers: 29959 At special positions: 0 Unit cell: (195.11, 154.78, 173.31, 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 2 29.99 S 113 16.00 P 67 15.00 Mg 1 11.99 O 5923 8.00 N 5372 7.00 C 18481 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: 13.79 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 6 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 46 sheets defined 38.9% alpha, 13.9% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 13.90 Creating SS restraints... Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.901A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 162 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 49 removed outlier: 4.029A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.750A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.537A pdb=" N ALA B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.502A pdb=" N LYS C 8 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 39 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.791A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.745A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.728A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.510A pdb=" N ILE C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.680A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.526A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.573A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.137A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.549A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.176A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.799A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.603A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.620A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.925A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.592A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.963A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 4.134A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.623A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.647A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.504A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.567A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.509A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.577A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.730A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.754A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.640A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.706A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.505A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.876A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.562A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.930A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.738A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.602A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 4.186A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.750A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 802 removed outlier: 3.931A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 807 removed outlier: 4.322A pdb=" N ASP D 806 " --> pdb=" O VAL D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 838 Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.814A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.696A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.930A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 4.169A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.558A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.663A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.203A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.657A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 Processing helix chain 'D' and resid 1328 through 1338 removed outlier: 3.630A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1362 through 1372 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.592A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.939A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 91 removed outlier: 3.635A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 33 Processing helix chain 'G' and resid 76 through 86 removed outlier: 4.080A pdb=" N VAL G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.538A pdb=" N VAL G 118 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 Processing helix chain 'F' and resid 19 through 39 removed outlier: 3.567A pdb=" N ILE F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 106 through 130 Processing helix chain 'F' and resid 201 through 212 removed outlier: 4.494A pdb=" N LEU F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 212 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 256 through 266 removed outlier: 3.688A pdb=" N THR F 264 " --> pdb=" O GLN F 260 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.868A pdb=" N ILE F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.798A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.566A pdb=" N ALA F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 364 removed outlier: 3.611A pdb=" N ASP F 364 " --> pdb=" O THR F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 375 Processing helix chain 'F' and resid 388 through 393 removed outlier: 3.556A pdb=" N LEU F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 402 Processing helix chain 'F' and resid 403 through 422 removed outlier: 3.694A pdb=" N ARG F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 411 " --> pdb=" O ARG F 407 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 425 No H-bonds generated for 'chain 'F' and resid 423 through 425' Processing helix chain 'F' and resid 442 through 452 removed outlier: 4.017A pdb=" N PHE F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 462 removed outlier: 3.867A pdb=" N LEU F 459 " --> pdb=" O THR F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 470 removed outlier: 3.734A pdb=" N ASP F 469 " --> pdb=" O ASP F 466 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 470 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 470' Processing helix chain 'F' and resid 474 through 491 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 6.426A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 7.375A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.528A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.893A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 4.916A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 201 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.484A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 57 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.694A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.594A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.283A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.742A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.619A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.646A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.636A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.571A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.267A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 749 through 752 removed outlier: 7.005A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 4.097A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C1098 " --> pdb=" O ALA C 803 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.699A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AC6, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.041A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 887 through 890 removed outlier: 4.776A pdb=" N ASP C 912 " --> pdb=" O LYS C 890 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.561A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.561A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.503A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.541A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 104 through 112 removed outlier: 10.123A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.845A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.021A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD6, first strand: chain 'D' and resid 555 through 556 Processing sheet with id=AD7, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.875A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.679A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE2, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.582A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 4.080A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1187 through 1190 Processing sheet with id=AE5, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AE6, first strand: chain 'G' and resid 39 through 42 removed outlier: 5.941A pdb=" N GLN G 72 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL G 42 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU G 70 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY G 91 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 45 through 49 removed outlier: 4.819A pdb=" N THR F 58 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 178 through 179 removed outlier: 3.906A pdb=" N VAL F 179 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY F 140 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL F 141 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP F 153 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER F 151 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL F 145 " --> pdb=" O ASN F 149 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN F 149 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 150 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE F 196 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 221 through 222 Processing sheet with id=AF1, first strand: chain 'F' and resid 227 through 229 removed outlier: 3.728A pdb=" N ALA F 227 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP F 272 " --> pdb=" O ALA F 234 " (cutoff:3.500A) 1144 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 19.47 Time building geometry restraints manager: 14.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10061 1.34 - 1.46: 4677 1.46 - 1.58: 15441 1.58 - 1.70: 130 1.70 - 1.82: 198 Bond restraints: 30507 Sorted by residual: bond pdb=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.52e+00 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.367 -0.034 2.34e-02 1.83e+03 2.05e+00 bond pdb=" C GLN C1061 " pdb=" N PRO C1062 " ideal model delta sigma weight residual 1.332 1.347 -0.015 1.12e-02 7.97e+03 1.74e+00 bond pdb=" C3' DC N 35 " pdb=" O3' DC N 35 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" C ALA C 910 " pdb=" N SER C 911 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.53e+00 ... (remaining 30502 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.46: 856 105.46 - 112.59: 15894 112.59 - 119.72: 10253 119.72 - 126.85: 14182 126.85 - 133.98: 401 Bond angle restraints: 41586 Sorted by residual: angle pdb=" N GLU E 76 " pdb=" CA GLU E 76 " pdb=" CB GLU E 76 " ideal model delta sigma weight residual 110.28 116.94 -6.66 1.55e+00 4.16e-01 1.84e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 128.92 -7.22 1.80e+00 3.09e-01 1.61e+01 angle pdb=" C GLN E 75 " pdb=" N GLU E 76 " pdb=" CA GLU E 76 " ideal model delta sigma weight residual 120.31 114.27 6.04 1.52e+00 4.33e-01 1.58e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 128.64 -6.94 1.80e+00 3.09e-01 1.48e+01 angle pdb=" C THR D 853 " pdb=" N ALA D 854 " pdb=" CA ALA D 854 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 ... (remaining 41581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 17760 29.06 - 58.12: 712 58.12 - 87.18: 90 87.18 - 116.23: 3 116.23 - 145.29: 3 Dihedral angle restraints: 18568 sinusoidal: 7565 harmonic: 11003 Sorted by residual: dihedral pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " ideal model delta harmonic sigma weight residual -180.00 -129.85 -50.15 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA SER B 141 " pdb=" C SER B 141 " pdb=" N MET B 142 " pdb=" CA MET B 142 " ideal model delta harmonic sigma weight residual 180.00 142.26 37.74 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA ARG A 166 " pdb=" C ARG A 166 " pdb=" N PRO A 167 " pdb=" CA PRO A 167 " ideal model delta harmonic sigma weight residual 180.00 149.93 30.07 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 18565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4183 0.063 - 0.127: 604 0.127 - 0.190: 28 0.190 - 0.253: 2 0.253 - 0.317: 3 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CB ILE B 140 " pdb=" CA ILE B 140 " pdb=" CG1 ILE B 140 " pdb=" CG2 ILE B 140 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 16 " pdb=" CA ILE B 16 " pdb=" CG1 ILE B 16 " pdb=" CG2 ILE B 16 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4817 not shown) Planarity restraints: 5266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " -0.065 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A 30 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 166 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 167 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO D 851 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.032 5.00e-02 4.00e+02 ... (remaining 5263 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 336 2.64 - 3.20: 26663 3.20 - 3.77: 45012 3.77 - 4.33: 57812 4.33 - 4.90: 94639 Nonbonded interactions: 224462 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.071 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.075 2.170 nonbonded pdb=" N2 DG N 37 " pdb=" O2 DC T 3 " model vdw 2.150 2.496 nonbonded pdb=" O LYS C 324 " pdb=" OG SER C 328 " model vdw 2.158 2.440 nonbonded pdb=" OH TYR D 679 " pdb=" O ILE D 754 " model vdw 2.172 2.440 ... (remaining 224457 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' and (resid 7 through 158 or resid 170 through 234)) selection = (chain 'B' and resid 7 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 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: 7.540 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 106.620 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.130 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:4.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30507 Z= 0.160 Angle : 0.620 11.663 41586 Z= 0.334 Chirality : 0.043 0.317 4820 Planarity : 0.004 0.100 5266 Dihedral : 15.152 145.293 11474 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 1.32 % Twisted General : 0.03 % 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: -1.41 (0.13), residues: 3812 helix: 0.24 (0.14), residues: 1295 sheet: -0.88 (0.26), residues: 393 loop : -1.76 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 236 HIS 0.009 0.001 HIS C1023 PHE 0.013 0.001 PHE G 65 TYR 0.017 0.001 TYR C1229 ARG 0.008 0.000 ARG D 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 3.349 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7596 (t70) cc_final: 0.7374 (t70) REVERT: A 137 ASN cc_start: 0.8060 (m-40) cc_final: 0.7487 (p0) REVERT: B 231 PHE cc_start: 0.7873 (m-10) cc_final: 0.7641 (m-10) REVERT: C 569 ILE cc_start: 0.9037 (tp) cc_final: 0.8802 (tt) REVERT: C 1023 HIS cc_start: 0.8171 (m-70) cc_final: 0.7719 (m-70) REVERT: C 1278 LEU cc_start: 0.9277 (tp) cc_final: 0.9067 (tp) REVERT: D 707 ILE cc_start: 0.8200 (mm) cc_final: 0.7967 (mt) REVERT: D 785 ASP cc_start: 0.8353 (t0) cc_final: 0.7996 (t70) REVERT: E 70 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8389 (mp10) REVERT: E 75 GLN cc_start: 0.8953 (pp30) cc_final: 0.8410 (pp30) REVERT: G 35 MET cc_start: 0.8418 (mpp) cc_final: 0.8194 (mpp) REVERT: G 90 MET cc_start: 0.7003 (mmm) cc_final: 0.6765 (mmm) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.3865 time to fit residues: 222.7974 Evaluate side-chains 241 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C1070 HIS ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 495 ASN D 777 HIS D 875 ASN D 979 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN G 33 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30507 Z= 0.234 Angle : 0.575 12.753 41586 Z= 0.300 Chirality : 0.042 0.181 4820 Planarity : 0.004 0.100 5266 Dihedral : 13.554 147.324 4930 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.16 % Allowed : 9.11 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -1.02 (0.13), residues: 3812 helix: 0.68 (0.14), residues: 1344 sheet: -0.70 (0.25), residues: 418 loop : -1.66 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 236 HIS 0.006 0.001 HIS C1070 PHE 0.021 0.002 PHE B 8 TYR 0.027 0.001 TYR B 177 ARG 0.004 0.000 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 259 time to evaluate : 3.538 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8339 (m110) cc_final: 0.8067 (m-40) REVERT: A 135 ASP cc_start: 0.7709 (t70) cc_final: 0.7390 (t70) REVERT: A 137 ASN cc_start: 0.8103 (m-40) cc_final: 0.7464 (p0) REVERT: B 35 PHE cc_start: 0.8179 (m-80) cc_final: 0.7835 (m-80) REVERT: B 231 PHE cc_start: 0.7984 (m-10) cc_final: 0.7681 (m-10) REVERT: C 130 MET cc_start: 0.8126 (mtp) cc_final: 0.7904 (mtp) REVERT: C 429 MET cc_start: 0.9099 (mtm) cc_final: 0.8791 (mtm) REVERT: C 569 ILE cc_start: 0.9193 (tp) cc_final: 0.8946 (tt) REVERT: C 636 CYS cc_start: 0.8231 (m) cc_final: 0.7971 (m) REVERT: C 768 MET cc_start: 0.7549 (mtm) cc_final: 0.7243 (mtm) REVERT: C 1023 HIS cc_start: 0.8215 (m-70) cc_final: 0.7767 (m-70) REVERT: C 1278 LEU cc_start: 0.9373 (tp) cc_final: 0.9112 (tp) REVERT: D 697 MET cc_start: 0.8489 (tmm) cc_final: 0.8182 (tmm) REVERT: D 821 MET cc_start: 0.7993 (tpt) cc_final: 0.7654 (mpp) REVERT: E 62 GLN cc_start: 0.8123 (tt0) cc_final: 0.7863 (tm-30) REVERT: G 35 MET cc_start: 0.8486 (mpp) cc_final: 0.8086 (mpp) outliers start: 33 outliers final: 23 residues processed: 279 average time/residue: 0.3806 time to fit residues: 179.8422 Evaluate side-chains 262 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 33 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 352 optimal weight: 50.0000 chunk 380 optimal weight: 50.0000 chunk 313 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 282 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D1108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30507 Z= 0.414 Angle : 0.675 9.168 41586 Z= 0.352 Chirality : 0.045 0.158 4820 Planarity : 0.005 0.100 5266 Dihedral : 13.681 147.459 4930 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.71 % Allowed : 13.51 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -1.17 (0.13), residues: 3812 helix: 0.66 (0.14), residues: 1329 sheet: -0.89 (0.24), residues: 437 loop : -1.78 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 236 HIS 0.019 0.002 HIS G 33 PHE 0.023 0.002 PHE C 390 TYR 0.032 0.002 TYR C1229 ARG 0.008 0.001 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 245 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.6829 (p90) REVERT: C 314 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.6969 (t0) REVERT: C 369 MET cc_start: 0.7673 (mmm) cc_final: 0.7469 (mmm) REVERT: C 429 MET cc_start: 0.9164 (mtm) cc_final: 0.8850 (mtm) REVERT: C 461 GLU cc_start: 0.8452 (tp30) cc_final: 0.7764 (tt0) REVERT: C 1023 HIS cc_start: 0.8261 (m-70) cc_final: 0.7762 (m-70) REVERT: C 1080 ASN cc_start: 0.8504 (t0) cc_final: 0.8146 (t0) REVERT: C 1085 MET cc_start: 0.9223 (mmt) cc_final: 0.8931 (mmp) REVERT: C 1119 MET cc_start: 0.8656 (tpp) cc_final: 0.7777 (tpp) REVERT: C 1122 LYS cc_start: 0.7507 (tttt) cc_final: 0.7094 (tttt) REVERT: D 581 MET cc_start: 0.8809 (tpp) cc_final: 0.8552 (ttm) REVERT: D 897 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7334 (t70) REVERT: D 1156 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8519 (tp) REVERT: D 1178 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7578 (p) REVERT: E 62 GLN cc_start: 0.8205 (tt0) cc_final: 0.7935 (tm-30) REVERT: E 75 GLN cc_start: 0.8837 (pp30) cc_final: 0.8569 (pp30) REVERT: G 33 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6722 (m-70) REVERT: G 35 MET cc_start: 0.8415 (mpp) cc_final: 0.8123 (mpp) REVERT: G 41 GLU cc_start: 0.8785 (pm20) cc_final: 0.8432 (pm20) outliers start: 77 outliers final: 40 residues processed: 303 average time/residue: 0.4055 time to fit residues: 205.1622 Evaluate side-chains 263 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 76 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 353 optimal weight: 10.0000 chunk 374 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 100 optimal weight: 0.0170 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN G 33 HIS G 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30507 Z= 0.167 Angle : 0.538 9.425 41586 Z= 0.281 Chirality : 0.041 0.148 4820 Planarity : 0.004 0.092 5266 Dihedral : 13.462 146.387 4930 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.18 % Allowed : 15.94 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -0.80 (0.14), residues: 3812 helix: 1.05 (0.15), residues: 1332 sheet: -0.63 (0.26), residues: 405 loop : -1.64 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.007 0.001 HIS D 80 PHE 0.027 0.001 PHE C 514 TYR 0.022 0.001 TYR G 10 ARG 0.005 0.000 ARG D 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 250 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8349 (tt0) cc_final: 0.8016 (tt0) REVERT: B 35 PHE cc_start: 0.8116 (m-80) cc_final: 0.7819 (m-80) REVERT: C 429 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8682 (mtm) REVERT: C 1023 HIS cc_start: 0.8344 (m-70) cc_final: 0.7883 (m-70) REVERT: C 1080 ASN cc_start: 0.8432 (t0) cc_final: 0.8174 (t0) REVERT: C 1119 MET cc_start: 0.8367 (tpp) cc_final: 0.7713 (tpp) REVERT: C 1229 TYR cc_start: 0.7653 (m-10) cc_final: 0.7217 (m-10) REVERT: C 1278 LEU cc_start: 0.9373 (tp) cc_final: 0.9097 (tp) REVERT: D 324 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7444 (pp) REVERT: D 475 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: D 581 MET cc_start: 0.8845 (tpp) cc_final: 0.8387 (ttm) REVERT: D 897 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7360 (t70) REVERT: D 1156 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 62 GLN cc_start: 0.8128 (tt0) cc_final: 0.7786 (tm-30) REVERT: E 75 GLN cc_start: 0.8821 (pp30) cc_final: 0.8557 (pp30) REVERT: G 35 MET cc_start: 0.8421 (mpp) cc_final: 0.8050 (mpp) outliers start: 62 outliers final: 35 residues processed: 295 average time/residue: 0.3964 time to fit residues: 199.1972 Evaluate side-chains 269 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 104 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 319 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 335 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS G 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30507 Z= 0.195 Angle : 0.549 13.664 41586 Z= 0.282 Chirality : 0.042 0.310 4820 Planarity : 0.004 0.090 5266 Dihedral : 13.391 146.876 4930 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.57 % Allowed : 16.71 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -0.70 (0.14), residues: 3812 helix: 1.18 (0.15), residues: 1330 sheet: -0.60 (0.25), residues: 419 loop : -1.62 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 236 HIS 0.009 0.001 HIS G 33 PHE 0.020 0.001 PHE C 514 TYR 0.020 0.001 TYR C1229 ARG 0.005 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 244 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.6733 (p90) REVERT: A 227 GLN cc_start: 0.8399 (tt0) cc_final: 0.8039 (tt0) REVERT: B 35 PHE cc_start: 0.8185 (m-80) cc_final: 0.7921 (m-80) REVERT: C 130 MET cc_start: 0.8235 (mtp) cc_final: 0.8001 (mtp) REVERT: C 429 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8750 (mtm) REVERT: C 488 MET cc_start: 0.6559 (ttp) cc_final: 0.6320 (ttp) REVERT: C 1023 HIS cc_start: 0.8351 (m-70) cc_final: 0.7903 (m-70) REVERT: C 1080 ASN cc_start: 0.8418 (t0) cc_final: 0.8201 (t0) REVERT: C 1119 MET cc_start: 0.8389 (tpp) cc_final: 0.7534 (tpp) REVERT: D 324 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7482 (pp) REVERT: D 581 MET cc_start: 0.8902 (tpp) cc_final: 0.8574 (ttm) REVERT: D 821 MET cc_start: 0.7914 (mpp) cc_final: 0.7667 (mpp) REVERT: D 897 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7462 (t70) REVERT: D 1156 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8436 (tp) REVERT: E 62 GLN cc_start: 0.8097 (tt0) cc_final: 0.7772 (tm-30) REVERT: E 75 GLN cc_start: 0.8758 (pp30) cc_final: 0.8532 (pp30) REVERT: G 10 TYR cc_start: 0.7604 (m-80) cc_final: 0.7389 (m-10) REVERT: G 35 MET cc_start: 0.8523 (mpp) cc_final: 0.8177 (mpp) outliers start: 73 outliers final: 52 residues processed: 296 average time/residue: 0.4124 time to fit residues: 209.6800 Evaluate side-chains 286 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 73 optimal weight: 0.0870 chunk 219 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 374 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 196 optimal weight: 0.5980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 365 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS G 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30507 Z= 0.150 Angle : 0.526 11.989 41586 Z= 0.271 Chirality : 0.041 0.319 4820 Planarity : 0.004 0.085 5266 Dihedral : 13.304 146.619 4930 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.81 % Allowed : 17.66 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -0.56 (0.14), residues: 3812 helix: 1.26 (0.15), residues: 1343 sheet: -0.48 (0.25), residues: 424 loop : -1.53 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 236 HIS 0.010 0.001 HIS G 33 PHE 0.021 0.001 PHE C1270 TYR 0.015 0.001 TYR A 177 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 257 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.6684 (p90) REVERT: B 35 PHE cc_start: 0.8144 (m-80) cc_final: 0.7901 (m-80) REVERT: C 130 MET cc_start: 0.8186 (mtp) cc_final: 0.7911 (mtp) REVERT: C 369 MET cc_start: 0.7662 (mmm) cc_final: 0.7446 (mmm) REVERT: C 429 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8778 (mtm) REVERT: C 766 ASN cc_start: 0.8774 (t0) cc_final: 0.8392 (t0) REVERT: C 1023 HIS cc_start: 0.8330 (m-70) cc_final: 0.7893 (m-70) REVERT: C 1080 ASN cc_start: 0.8419 (t0) cc_final: 0.8035 (t0) REVERT: C 1085 MET cc_start: 0.9066 (mmt) cc_final: 0.8681 (mmp) REVERT: C 1119 MET cc_start: 0.8382 (tpp) cc_final: 0.7537 (tpp) REVERT: C 1270 PHE cc_start: 0.8266 (t80) cc_final: 0.8035 (t80) REVERT: C 1304 MET cc_start: 0.8492 (tpp) cc_final: 0.8191 (ttm) REVERT: D 304 ASP cc_start: 0.7055 (p0) cc_final: 0.6845 (p0) REVERT: D 475 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: D 707 ILE cc_start: 0.8579 (mm) cc_final: 0.8008 (mt) REVERT: D 897 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7375 (t70) REVERT: D 1156 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8384 (tp) REVERT: E 62 GLN cc_start: 0.8066 (tt0) cc_final: 0.7548 (tm-30) REVERT: G 33 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.6875 (m170) REVERT: G 35 MET cc_start: 0.8506 (mpp) cc_final: 0.8290 (mmm) outliers start: 80 outliers final: 53 residues processed: 314 average time/residue: 0.3832 time to fit residues: 205.0840 Evaluate side-chains 297 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 238 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 585 LYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 213 optimal weight: 0.2980 chunk 273 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 373 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30507 Z= 0.181 Angle : 0.540 12.052 41586 Z= 0.276 Chirality : 0.042 0.348 4820 Planarity : 0.004 0.086 5266 Dihedral : 13.282 146.981 4930 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.96 % Allowed : 18.37 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -0.51 (0.14), residues: 3812 helix: 1.33 (0.15), residues: 1336 sheet: -0.39 (0.25), residues: 417 loop : -1.52 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1276 HIS 0.008 0.001 HIS G 33 PHE 0.018 0.001 PHE C1270 TYR 0.015 0.001 TYR A 177 ARG 0.004 0.000 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 248 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.6640 (p90) REVERT: C 369 MET cc_start: 0.7613 (mmm) cc_final: 0.7385 (mmm) REVERT: C 429 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8817 (mtm) REVERT: C 766 ASN cc_start: 0.8770 (t0) cc_final: 0.8396 (t0) REVERT: C 1023 HIS cc_start: 0.8289 (m-70) cc_final: 0.7851 (m-70) REVERT: C 1080 ASN cc_start: 0.8458 (t0) cc_final: 0.8207 (t0) REVERT: C 1085 MET cc_start: 0.9127 (mmt) cc_final: 0.8823 (mmp) REVERT: C 1119 MET cc_start: 0.8435 (tpp) cc_final: 0.7616 (tpp) REVERT: C 1304 MET cc_start: 0.8589 (tpp) cc_final: 0.8317 (ttm) REVERT: D 304 ASP cc_start: 0.7084 (p0) cc_final: 0.6844 (p0) REVERT: D 324 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7463 (pp) REVERT: D 475 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: D 897 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7435 (t70) REVERT: D 1040 MET cc_start: 0.5657 (ptp) cc_final: 0.5399 (ptt) REVERT: E 62 GLN cc_start: 0.8082 (tt0) cc_final: 0.7563 (tm-30) outliers start: 84 outliers final: 61 residues processed: 309 average time/residue: 0.3821 time to fit residues: 201.7765 Evaluate side-chains 303 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 237 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 585 LYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 994 SER Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 112 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30507 Z= 0.191 Angle : 0.553 12.552 41586 Z= 0.282 Chirality : 0.042 0.359 4820 Planarity : 0.004 0.097 5266 Dihedral : 13.270 146.943 4930 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.74 % Allowed : 19.18 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -0.48 (0.14), residues: 3812 helix: 1.35 (0.15), residues: 1335 sheet: -0.50 (0.25), residues: 436 loop : -1.48 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 236 HIS 0.005 0.001 HIS G 33 PHE 0.022 0.001 PHE C 157 TYR 0.015 0.001 TYR A 177 ARG 0.004 0.000 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 245 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.6696 (p90) REVERT: C 130 MET cc_start: 0.8237 (mtp) cc_final: 0.7981 (mtp) REVERT: C 369 MET cc_start: 0.7616 (mmm) cc_final: 0.7366 (mmm) REVERT: C 429 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8819 (mtm) REVERT: C 461 GLU cc_start: 0.8233 (tp30) cc_final: 0.7642 (tt0) REVERT: C 766 ASN cc_start: 0.8777 (t0) cc_final: 0.8403 (t0) REVERT: C 1023 HIS cc_start: 0.8237 (m-70) cc_final: 0.7806 (m-70) REVERT: C 1080 ASN cc_start: 0.8485 (t0) cc_final: 0.8230 (t0) REVERT: C 1085 MET cc_start: 0.9141 (mmt) cc_final: 0.8858 (mmp) REVERT: C 1119 MET cc_start: 0.8482 (tpp) cc_final: 0.7700 (tpp) REVERT: C 1274 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: C 1304 MET cc_start: 0.8583 (tpp) cc_final: 0.8295 (tpp) REVERT: D 237 MET cc_start: 0.8688 (mmm) cc_final: 0.8455 (mmm) REVERT: D 324 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7515 (pp) REVERT: D 475 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: D 897 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7433 (t70) REVERT: D 1156 LEU cc_start: 0.8818 (mm) cc_final: 0.8437 (tp) REVERT: D 1196 LEU cc_start: 0.8336 (tt) cc_final: 0.7801 (mt) REVERT: E 62 GLN cc_start: 0.8094 (tt0) cc_final: 0.7569 (tm-30) outliers start: 78 outliers final: 63 residues processed: 302 average time/residue: 0.3787 time to fit residues: 194.9858 Evaluate side-chains 307 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 238 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 585 LYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 994 SER Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 50.0000 chunk 357 optimal weight: 30.0000 chunk 326 optimal weight: 20.0000 chunk 347 optimal weight: 50.0000 chunk 209 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 346 optimal weight: 50.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 227 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 495 ASN D1238 GLN G 33 HIS G 72 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.097 30507 Z= 0.621 Angle : 0.826 11.439 41586 Z= 0.425 Chirality : 0.049 0.315 4820 Planarity : 0.006 0.103 5266 Dihedral : 13.680 147.378 4930 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.08 % Favored : 91.89 % Rotamer: Outliers : 3.31 % Allowed : 19.21 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -1.20 (0.13), residues: 3812 helix: 0.67 (0.14), residues: 1329 sheet: -1.05 (0.24), residues: 441 loop : -1.80 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 807 HIS 0.010 0.002 HIS G 33 PHE 0.031 0.003 PHE C 390 TYR 0.026 0.003 TYR B 177 ARG 0.010 0.001 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 230 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.6023 (m-30) cc_final: 0.5682 (m-30) REVERT: A 177 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.6934 (p90) REVERT: A 207 THR cc_start: 0.8852 (m) cc_final: 0.8534 (p) REVERT: C 429 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8774 (mtm) REVERT: C 461 GLU cc_start: 0.8546 (tp30) cc_final: 0.8004 (tm-30) REVERT: C 488 MET cc_start: 0.7000 (ttp) cc_final: 0.6752 (ttp) REVERT: C 766 ASN cc_start: 0.8738 (t0) cc_final: 0.8396 (t0) REVERT: C 1023 HIS cc_start: 0.8243 (m-70) cc_final: 0.7826 (m-70) REVERT: C 1080 ASN cc_start: 0.8613 (t0) cc_final: 0.8385 (t0) REVERT: C 1119 MET cc_start: 0.8734 (tpp) cc_final: 0.8110 (tpp) REVERT: C 1274 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: C 1304 MET cc_start: 0.8734 (tpp) cc_final: 0.8435 (ttm) REVERT: D 237 MET cc_start: 0.8913 (mmm) cc_final: 0.8689 (tpp) REVERT: D 324 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8210 (pp) REVERT: D 897 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7217 (t70) REVERT: D 1040 MET cc_start: 0.7585 (ptt) cc_final: 0.7138 (ppp) REVERT: E 62 GLN cc_start: 0.8212 (tt0) cc_final: 0.7931 (tm-30) outliers start: 94 outliers final: 65 residues processed: 296 average time/residue: 0.3712 time to fit residues: 187.1965 Evaluate side-chains 292 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 222 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 994 SER Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 0.6980 chunk 367 optimal weight: 40.0000 chunk 224 optimal weight: 0.0970 chunk 174 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 385 optimal weight: 50.0000 chunk 354 optimal weight: 40.0000 chunk 307 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 237 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.327 30507 Z= 0.455 Angle : 0.905 58.947 41586 Z= 0.479 Chirality : 0.048 0.443 4820 Planarity : 0.006 0.106 5266 Dihedral : 13.680 147.673 4930 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.71 % Allowed : 20.16 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -1.23 (0.13), residues: 3812 helix: 0.66 (0.14), residues: 1329 sheet: -1.09 (0.24), residues: 441 loop : -1.82 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 236 HIS 0.090 0.003 HIS G 33 PHE 0.033 0.003 PHE B 35 TYR 0.114 0.003 TYR D 555 ARG 0.010 0.001 ARG C 974 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 224 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8775 (p90) REVERT: A 62 ASP cc_start: 0.5990 (m-30) cc_final: 0.5655 (m-30) REVERT: A 177 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.6844 (p90) REVERT: A 207 THR cc_start: 0.8822 (m) cc_final: 0.8503 (p) REVERT: C 130 MET cc_start: 0.8305 (mtp) cc_final: 0.8096 (mtp) REVERT: C 429 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8785 (mtm) REVERT: C 461 GLU cc_start: 0.8505 (tp30) cc_final: 0.7959 (tm-30) REVERT: C 766 ASN cc_start: 0.8691 (t0) cc_final: 0.8331 (t0) REVERT: C 1023 HIS cc_start: 0.8234 (m-70) cc_final: 0.7817 (m-70) REVERT: C 1119 MET cc_start: 0.8677 (tpp) cc_final: 0.8067 (tpp) REVERT: C 1274 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: C 1304 MET cc_start: 0.8705 (tpp) cc_final: 0.8384 (ttm) REVERT: D 237 MET cc_start: 0.8895 (mmm) cc_final: 0.8680 (tpp) REVERT: D 324 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (pp) REVERT: D 432 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8603 (mm) REVERT: D 897 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7190 (t70) REVERT: D 1040 MET cc_start: 0.7513 (ptt) cc_final: 0.7074 (ppp) REVERT: E 62 GLN cc_start: 0.8214 (tt0) cc_final: 0.7921 (tm-30) outliers start: 77 outliers final: 66 residues processed: 281 average time/residue: 0.3880 time to fit residues: 185.1692 Evaluate side-chains 296 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 223 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 994 SER Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 0.8980 chunk 327 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 307 optimal weight: 0.0970 chunk 128 optimal weight: 0.7980 chunk 315 optimal weight: 0.0980 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D1108 GLN G 33 HIS G 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.144602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099222 restraints weight = 57762.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098762 restraints weight = 36267.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099003 restraints weight = 26649.770| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30507 Z= 0.187 Angle : 0.602 15.842 41586 Z= 0.309 Chirality : 0.043 0.343 4820 Planarity : 0.004 0.101 5266 Dihedral : 13.462 147.338 4930 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.18 % Allowed : 20.76 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -0.81 (0.14), residues: 3812 helix: 1.06 (0.15), residues: 1329 sheet: -0.81 (0.25), residues: 435 loop : -1.62 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 236 HIS 0.033 0.001 HIS A 23 PHE 0.017 0.001 PHE C 514 TYR 0.016 0.001 TYR A 177 ARG 0.004 0.000 ARG C 974 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5492.81 seconds wall clock time: 102 minutes 16.16 seconds (6136.16 seconds total)