Starting phenix.real_space_refine on Tue Feb 20 09:03:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py1_13707/02_2024/7py1_13707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py1_13707/02_2024/7py1_13707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py1_13707/02_2024/7py1_13707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py1_13707/02_2024/7py1_13707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py1_13707/02_2024/7py1_13707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py1_13707/02_2024/7py1_13707.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 16966 2.51 5 N 4863 2.21 5 O 5422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 516": "OD1" <-> "OD2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "C GLU 968": "OE1" <-> "OE2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C ASP 1188": "OD1" <-> "OD2" Residue "C PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1241": "OD1" <-> "OD2" Residue "C GLU 1279": "OE1" <-> "OE2" Residue "C GLU 1289": "OE1" <-> "OE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D ASP 622": "OD1" <-> "OD2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 827": "OE1" <-> "OE2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1236": "OE1" <-> "OE2" Residue "D GLU 1317": "OE1" <-> "OE2" Residue "D GLU 1334": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27442 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 620 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "T" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} 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: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1706 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "C" Number of atoms: 10548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10548 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1280} Chain breaks: 1 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: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} 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: "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 15931 SG CYS D 70 23.808 56.226 95.610 1.00117.23 S ATOM 15945 SG CYS D 72 24.017 53.800 98.142 1.00121.27 S ATOM 21765 SG CYS D 814 44.027 122.965 90.186 1.00 81.42 S ATOM 22330 SG CYS D 888 45.127 118.500 90.716 1.00 69.27 S ATOM 22381 SG CYS D 895 43.791 120.121 87.625 1.00 59.88 S ATOM 22402 SG CYS D 898 46.845 121.099 88.703 1.00 57.14 S Time building chain proxies: 14.07, per 1000 atoms: 0.51 Number of scatterers: 27442 At special positions: 0 Unit cell: (135.3, 167.2, 169.4, 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 75 15.00 Mg 1 11.99 O 5422 8.00 N 4863 7.00 C 16966 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: 11.71 Conformation dependent library (CDL) restraints added in 5.1 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 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 52 sheets defined 36.0% alpha, 14.6% beta 32 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 8.61 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 4.280A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) 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 212 through 230 removed outlier: 3.834A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.926A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.951A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (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 229 removed outlier: 3.712A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.709A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.985A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.177A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.916A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.631A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.787A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.515A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.632A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 614' Processing helix chain 'C' and resid 663 through 668 removed outlier: 4.014A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) 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 removed outlier: 4.006A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 942 through 977 removed outlier: 3.547A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 965 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.882A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.552A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.728A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.042A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.265A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1175 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.750A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.547A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1299 through 1309 removed outlier: 3.648A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.814A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.614A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.028A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.614A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.955A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (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 284 removed outlier: 3.794A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 408 through 415 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 452 through 458 removed outlier: 4.086A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.565A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.875A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 4.223A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 4.090A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.838A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.566A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.921A 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 removed outlier: 3.535A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.135A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.609A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.584A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.753A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 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: 3.545A 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 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.501A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.568A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.814A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.634A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.589A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.544A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.659A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 77 through 86 removed outlier: 3.609A pdb=" N VAL G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.384A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.384A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU A 198 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA A 189 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.591A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 143 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.750A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.090A 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 13 removed outlier: 3.707A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.707A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 188 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 204 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.998A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 100 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.816A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 4.013A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.769A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 4.958A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.650A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.126A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 removed outlier: 4.308A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 228 through 231 removed outlier: 3.526A pdb=" N THR C 335 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.512A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.827A pdb=" N ALA C 257 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.019A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.696A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.846A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.502A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 634 through 636 Processing sheet with id=AC7, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.146A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 750 through 752 removed outlier: 3.598A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.518A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'C' and resid 1076 through 1080 removed outlier: 7.484A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.322A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.674A pdb=" N LEU C 883 " --> pdb=" O LEU C 918 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 887 through 888 removed outlier: 3.561A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.505A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 468 " --> pdb=" O GLY D 351 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 421 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.505A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.675A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 104 through 112 removed outlier: 3.518A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'D' and resid 366 through 368 removed outlier: 6.568A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.048A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE5, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.638A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 825 through 826 removed outlier: 7.342A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.764A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 991 through 995 removed outlier: 4.177A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AF1, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.579A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1046 through 1048 Processing sheet with id=AF3, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.657A pdb=" N ILE D1155 " --> pdb=" O ILE D1210 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1175 through 1178 Processing sheet with id=AF5, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.595A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 68 through 71 removed outlier: 4.503A pdb=" N GLY G 91 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 47 through 48 929 hydrogen bonds defined for protein. 2601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 13.62 Time building geometry restraints manager: 12.36 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: 8931 1.34 - 1.46: 3861 1.46 - 1.58: 14872 1.58 - 1.70: 146 1.70 - 1.82: 198 Bond restraints: 28008 Sorted by residual: bond pdb=" CA THR D 514 " pdb=" CB THR D 514 " ideal model delta sigma weight residual 1.528 1.548 -0.020 1.39e-02 5.18e+03 2.17e+00 bond pdb=" C3' DC T 3 " pdb=" O3' DC T 3 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CA GLN C 36 " pdb=" CB GLN C 36 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.15e-02 7.56e+03 1.94e+00 bond pdb=" N HIS C1023 " pdb=" CA HIS C1023 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.20e-02 6.94e+03 1.55e+00 bond pdb=" C3' DC N 35 " pdb=" O3' DC N 35 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.45e+00 ... (remaining 28003 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.35: 1109 106.35 - 113.27: 15268 113.27 - 120.18: 9843 120.18 - 127.10: 11571 127.10 - 134.01: 350 Bond angle restraints: 38141 Sorted by residual: angle pdb=" CA TYR C1018 " pdb=" CB TYR C1018 " pdb=" CG TYR C1018 " ideal model delta sigma weight residual 113.90 122.12 -8.22 1.80e+00 3.09e-01 2.08e+01 angle pdb=" N GLN C 36 " pdb=" CA GLN C 36 " pdb=" C GLN C 36 " ideal model delta sigma weight residual 113.20 107.68 5.52 1.36e+00 5.41e-01 1.65e+01 angle pdb=" CB LYS C1022 " pdb=" CG LYS C1022 " pdb=" CD LYS C1022 " ideal model delta sigma weight residual 111.30 120.37 -9.07 2.30e+00 1.89e-01 1.56e+01 angle pdb=" N GLU G 28 " pdb=" CA GLU G 28 " pdb=" CB GLU G 28 " ideal model delta sigma weight residual 110.28 116.19 -5.91 1.55e+00 4.16e-01 1.45e+01 angle pdb=" N VAL A 19 " pdb=" CA VAL A 19 " pdb=" C VAL A 19 " ideal model delta sigma weight residual 113.53 109.86 3.67 9.80e-01 1.04e+00 1.40e+01 ... (remaining 38136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 16501 35.17 - 70.34: 529 70.34 - 105.51: 40 105.51 - 140.68: 1 140.68 - 175.85: 4 Dihedral angle restraints: 17075 sinusoidal: 7590 harmonic: 9485 Sorted by residual: dihedral pdb=" CA ASP C1150 " pdb=" C ASP C1150 " pdb=" N LEU C1151 " pdb=" CA LEU C1151 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLY D 173 " pdb=" C GLY D 173 " pdb=" N ASP D 174 " pdb=" CA ASP D 174 " ideal model delta harmonic sigma weight residual 180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER D 503 " pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 17072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3370 0.044 - 0.087: 716 0.087 - 0.131: 254 0.131 - 0.175: 7 0.175 - 0.219: 4 Chirality restraints: 4351 Sorted by residual: chirality pdb=" CA LYS C1022 " pdb=" N LYS C1022 " pdb=" C LYS C1022 " pdb=" CB LYS C1022 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA GLU G 28 " pdb=" N GLU G 28 " pdb=" C GLU G 28 " pdb=" CB GLU G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" C3' U R 4 " pdb=" C4' U R 4 " pdb=" O3' U R 4 " pdb=" C2' U R 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 4348 not shown) Planarity restraints: 4731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 177 " 0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO C 178 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO D 288 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 125 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 126 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.029 5.00e-02 4.00e+02 ... (remaining 4728 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 737 2.70 - 3.25: 26800 3.25 - 3.80: 41539 3.80 - 4.35: 50526 4.35 - 4.90: 83440 Nonbonded interactions: 203042 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.154 2.170 nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.177 2.170 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.187 2.310 nonbonded pdb=" O VAL C 884 " pdb=" OG SER C 917 " model vdw 2.222 2.440 nonbonded pdb=" O GLN C1013 " pdb=" NE2 GLN C1017 " model vdw 2.230 2.520 ... (remaining 203037 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 232)) selection = (chain 'B' and resid 7 through 232) } 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: 1.090 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: 5.980 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 83.820 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 0.044 28008 Z= 0.145 Angle : 0.563 9.071 38141 Z= 0.302 Chirality : 0.041 0.219 4351 Planarity : 0.004 0.087 4731 Dihedral : 16.560 175.852 10973 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.04 % Allowed : 0.11 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3285 helix: 1.17 (0.17), residues: 1052 sheet: -0.26 (0.29), residues: 324 loop : -1.38 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 997 HIS 0.011 0.001 HIS G 29 PHE 0.019 0.001 PHE D1325 TYR 0.032 0.001 TYR C1018 ARG 0.012 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 722 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6439 (mt-10) REVERT: A 143 ARG cc_start: 0.6920 (mpp80) cc_final: 0.5948 (mtm-85) REVERT: A 204 GLU cc_start: 0.7368 (pp20) cc_final: 0.7132 (pp20) REVERT: B 58 GLU cc_start: 0.7414 (pt0) cc_final: 0.7059 (pt0) REVERT: B 80 GLU cc_start: 0.7382 (tp30) cc_final: 0.7180 (tp30) REVERT: B 110 VAL cc_start: 0.7785 (t) cc_final: 0.7535 (t) REVERT: B 123 ILE cc_start: 0.8471 (mp) cc_final: 0.7643 (mp) REVERT: B 185 TYR cc_start: 0.8564 (p90) cc_final: 0.8236 (p90) REVERT: B 200 LYS cc_start: 0.8446 (tttm) cc_final: 0.7998 (tttm) REVERT: B 227 GLN cc_start: 0.7552 (tp40) cc_final: 0.7057 (tp40) REVERT: C 14 ASP cc_start: 0.7047 (t0) cc_final: 0.6702 (t0) REVERT: C 84 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 101 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7510 (ttm-80) REVERT: C 122 VAL cc_start: 0.8375 (m) cc_final: 0.7815 (p) REVERT: C 124 MET cc_start: 0.7047 (ptm) cc_final: 0.6508 (ppp) REVERT: C 158 ASP cc_start: 0.7173 (m-30) cc_final: 0.6943 (m-30) REVERT: C 160 ASP cc_start: 0.6726 (t70) cc_final: 0.6223 (t0) REVERT: C 179 TYR cc_start: 0.7173 (t80) cc_final: 0.6856 (t80) REVERT: C 180 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7430 (ttp-170) REVERT: C 196 VAL cc_start: 0.7785 (t) cc_final: 0.7544 (p) REVERT: C 208 ILE cc_start: 0.7250 (pt) cc_final: 0.7044 (mp) REVERT: C 316 GLU cc_start: 0.7168 (tt0) cc_final: 0.6962 (tt0) REVERT: C 337 PHE cc_start: 0.6914 (t80) cc_final: 0.6483 (t80) REVERT: C 386 GLU cc_start: 0.7517 (tp30) cc_final: 0.7269 (tp30) REVERT: C 429 MET cc_start: 0.7262 (tpp) cc_final: 0.6858 (tpt) REVERT: C 441 GLU cc_start: 0.6867 (tp30) cc_final: 0.6600 (tp30) REVERT: C 478 ARG cc_start: 0.7817 (tpt90) cc_final: 0.7477 (tpt90) REVERT: C 481 LEU cc_start: 0.7435 (mt) cc_final: 0.6822 (tt) REVERT: C 504 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 568 ASN cc_start: 0.8193 (p0) cc_final: 0.7598 (p0) REVERT: C 584 TYR cc_start: 0.8472 (m-10) cc_final: 0.8011 (m-10) REVERT: C 636 CYS cc_start: 0.7956 (m) cc_final: 0.7665 (m) REVERT: C 641 GLU cc_start: 0.6765 (pp20) cc_final: 0.6377 (pp20) REVERT: C 717 VAL cc_start: 0.8322 (p) cc_final: 0.7903 (t) REVERT: C 719 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7415 (mtmm) REVERT: C 741 MET cc_start: 0.7109 (ttp) cc_final: 0.6815 (ttp) REVERT: C 793 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6695 (mt-10) REVERT: C 800 MET cc_start: 0.8209 (pmm) cc_final: 0.7898 (pmm) REVERT: C 848 GLU cc_start: 0.6602 (pt0) cc_final: 0.6201 (pt0) REVERT: C 930 ASP cc_start: 0.7577 (t70) cc_final: 0.7290 (t70) REVERT: C 950 GLU cc_start: 0.8088 (tp30) cc_final: 0.7420 (tp30) REVERT: C 951 MET cc_start: 0.7609 (mtp) cc_final: 0.7093 (mtp) REVERT: C 957 LYS cc_start: 0.8520 (tppt) cc_final: 0.8216 (tppt) REVERT: C 1032 LYS cc_start: 0.8438 (ptpp) cc_final: 0.8201 (pttt) REVERT: C 1033 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7803 (ptm-80) REVERT: C 1064 ASP cc_start: 0.8118 (t0) cc_final: 0.7682 (t70) REVERT: C 1066 MET cc_start: 0.7157 (ttp) cc_final: 0.6903 (ttp) REVERT: C 1083 GLU cc_start: 0.7314 (pm20) cc_final: 0.7106 (pm20) REVERT: C 1131 MET cc_start: 0.7757 (ttm) cc_final: 0.7463 (ttp) REVERT: C 1160 ASP cc_start: 0.7546 (p0) cc_final: 0.7289 (p0) REVERT: C 1168 GLU cc_start: 0.7347 (pt0) cc_final: 0.6990 (pm20) REVERT: C 1188 ASP cc_start: 0.7262 (t0) cc_final: 0.7026 (t0) REVERT: C 1200 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8157 (ttpp) REVERT: C 1219 GLU cc_start: 0.7207 (pp20) cc_final: 0.6901 (pp20) REVERT: C 1220 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: C 1240 ASP cc_start: 0.7972 (p0) cc_final: 0.7632 (p0) REVERT: C 1241 ASP cc_start: 0.7508 (m-30) cc_final: 0.6816 (t0) REVERT: C 1304 MET cc_start: 0.7795 (ttp) cc_final: 0.7514 (ttt) REVERT: D 26 SER cc_start: 0.8434 (p) cc_final: 0.8216 (m) REVERT: D 33 TRP cc_start: 0.7051 (m-10) cc_final: 0.6547 (m-10) REVERT: D 53 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6857 (mtp-110) REVERT: D 74 LYS cc_start: 0.7918 (tmmt) cc_final: 0.7684 (tptp) REVERT: D 88 CYS cc_start: 0.6588 (t) cc_final: 0.5242 (t) REVERT: D 130 MET cc_start: 0.7014 (mtt) cc_final: 0.6663 (mtp) REVERT: D 146 VAL cc_start: 0.8389 (t) cc_final: 0.8045 (p) REVERT: D 148 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7097 (tm-30) REVERT: D 162 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7365 (mm-30) REVERT: D 176 PHE cc_start: 0.7199 (p90) cc_final: 0.6844 (p90) REVERT: D 192 MET cc_start: 0.8022 (ttp) cc_final: 0.7284 (tmm) REVERT: D 200 GLN cc_start: 0.7774 (pp30) cc_final: 0.7500 (pp30) REVERT: D 204 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 216 LYS cc_start: 0.7571 (tttm) cc_final: 0.6980 (tttm) REVERT: D 222 LYS cc_start: 0.8070 (tmtt) cc_final: 0.7667 (tptp) REVERT: D 291 ILE cc_start: 0.7917 (mm) cc_final: 0.7687 (mm) REVERT: D 399 LYS cc_start: 0.8137 (tmmt) cc_final: 0.7585 (tmmt) REVERT: D 462 ASP cc_start: 0.7380 (p0) cc_final: 0.7178 (p0) REVERT: D 497 GLU cc_start: 0.7296 (pp20) cc_final: 0.7068 (pp20) REVERT: D 528 THR cc_start: 0.8111 (m) cc_final: 0.7908 (m) REVERT: D 591 ILE cc_start: 0.8188 (tp) cc_final: 0.7907 (pt) REVERT: D 667 GLN cc_start: 0.7869 (tt0) cc_final: 0.7594 (tm-30) REVERT: D 695 LYS cc_start: 0.8324 (tmmt) cc_final: 0.7879 (tmmt) REVERT: D 698 MET cc_start: 0.7882 (tpp) cc_final: 0.7633 (mmm) REVERT: D 715 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7853 (mtmt) REVERT: D 723 TYR cc_start: 0.7694 (t80) cc_final: 0.7429 (t80) REVERT: D 795 TYR cc_start: 0.8030 (t80) cc_final: 0.7699 (t80) REVERT: D 802 ASP cc_start: 0.7142 (t0) cc_final: 0.6854 (t0) REVERT: D 805 GLN cc_start: 0.7591 (pp30) cc_final: 0.7385 (pp30) REVERT: D 867 GLN cc_start: 0.7733 (tm-30) cc_final: 0.6917 (tm-30) REVERT: D 915 ILE cc_start: 0.8767 (tt) cc_final: 0.8553 (tp) REVERT: D 951 GLN cc_start: 0.7848 (tp40) cc_final: 0.7509 (tp40) REVERT: D 992 LYS cc_start: 0.7404 (mptt) cc_final: 0.7203 (mmtt) REVERT: D 1040 MET cc_start: 0.2061 (ttt) cc_final: 0.1774 (ttp) REVERT: D 1155 ILE cc_start: 0.8506 (mp) cc_final: 0.8266 (mp) REVERT: D 1173 ARG cc_start: 0.4292 (mtm-85) cc_final: 0.3860 (mpp-170) REVERT: D 1175 LEU cc_start: 0.6595 (tt) cc_final: 0.6273 (tt) REVERT: D 1240 VAL cc_start: 0.7808 (t) cc_final: 0.7577 (p) REVERT: E 66 VAL cc_start: 0.9025 (t) cc_final: 0.8815 (p) REVERT: G 43 MET cc_start: 0.6826 (ppp) cc_final: 0.6223 (ppp) REVERT: G 82 LEU cc_start: 0.7302 (mt) cc_final: 0.7041 (mp) outliers start: 1 outliers final: 0 residues processed: 723 average time/residue: 0.4468 time to fit residues: 481.0853 Evaluate side-chains 639 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 638 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1220 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 195 optimal weight: 0.0030 chunk 304 optimal weight: 0.0970 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 613 ASN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN D 504 GLN D 716 GLN D 865 HIS D 929 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS G 34 ASN G 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28008 Z= 0.171 Angle : 0.567 7.647 38141 Z= 0.295 Chirality : 0.042 0.195 4351 Planarity : 0.004 0.064 4731 Dihedral : 14.880 174.116 4491 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 1.17 % Allowed : 11.95 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3285 helix: 1.27 (0.16), residues: 1081 sheet: -0.00 (0.28), residues: 348 loop : -1.30 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 997 HIS 0.005 0.001 HIS D1218 PHE 0.035 0.001 PHE C 38 TYR 0.031 0.001 TYR D1232 ARG 0.008 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 675 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.6993 (mpp80) cc_final: 0.6702 (mpp80) REVERT: A 204 GLU cc_start: 0.7341 (pp20) cc_final: 0.7089 (pp20) REVERT: A 215 GLU cc_start: 0.7305 (tm-30) cc_final: 0.7040 (mm-30) REVERT: B 44 ARG cc_start: 0.8228 (tmm-80) cc_final: 0.7816 (ttm170) REVERT: B 58 GLU cc_start: 0.7343 (pt0) cc_final: 0.6927 (tt0) REVERT: B 76 GLU cc_start: 0.6586 (pm20) cc_final: 0.6149 (pm20) REVERT: B 96 ASP cc_start: 0.6603 (t70) cc_final: 0.6311 (t70) REVERT: B 174 ASP cc_start: 0.7603 (m-30) cc_final: 0.7257 (m-30) REVERT: B 200 LYS cc_start: 0.8471 (tttm) cc_final: 0.8038 (tttm) REVERT: B 227 GLN cc_start: 0.7706 (tp40) cc_final: 0.7256 (tp40) REVERT: C 14 ASP cc_start: 0.7184 (t0) cc_final: 0.6739 (t0) REVERT: C 36 GLN cc_start: 0.7656 (tp40) cc_final: 0.6540 (tm-30) REVERT: C 101 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.6709 (ttm-80) REVERT: C 124 MET cc_start: 0.6675 (ptm) cc_final: 0.6259 (ppp) REVERT: C 158 ASP cc_start: 0.7069 (m-30) cc_final: 0.6862 (m-30) REVERT: C 160 ASP cc_start: 0.6927 (t70) cc_final: 0.6367 (t0) REVERT: C 179 TYR cc_start: 0.7222 (t80) cc_final: 0.6897 (t80) REVERT: C 180 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7437 (ttp-170) REVERT: C 196 VAL cc_start: 0.7648 (t) cc_final: 0.7428 (p) REVERT: C 234 ASP cc_start: 0.8339 (p0) cc_final: 0.8074 (p0) REVERT: C 337 PHE cc_start: 0.6989 (t80) cc_final: 0.6404 (t80) REVERT: C 429 MET cc_start: 0.7372 (tpp) cc_final: 0.6919 (tpt) REVERT: C 441 GLU cc_start: 0.6902 (tp30) cc_final: 0.6669 (tp30) REVERT: C 478 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7530 (tpt90) REVERT: C 481 LEU cc_start: 0.7440 (mt) cc_final: 0.6838 (tt) REVERT: C 488 MET cc_start: 0.6900 (mpp) cc_final: 0.6334 (mpp) REVERT: C 568 ASN cc_start: 0.8201 (p0) cc_final: 0.7629 (p0) REVERT: C 636 CYS cc_start: 0.7794 (m) cc_final: 0.7327 (m) REVERT: C 641 GLU cc_start: 0.6818 (pp20) cc_final: 0.6398 (pp20) REVERT: C 717 VAL cc_start: 0.8268 (p) cc_final: 0.7977 (t) REVERT: C 719 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7497 (mtmm) REVERT: C 720 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7190 (mtt-85) REVERT: C 738 GLU cc_start: 0.6872 (tp30) cc_final: 0.6618 (tp30) REVERT: C 761 GLN cc_start: 0.8041 (mm110) cc_final: 0.7788 (mm-40) REVERT: C 800 MET cc_start: 0.8090 (pmm) cc_final: 0.7313 (ptp) REVERT: C 805 MET cc_start: 0.7172 (ttm) cc_final: 0.6870 (ttm) REVERT: C 848 GLU cc_start: 0.6503 (pt0) cc_final: 0.6033 (pt0) REVERT: C 930 ASP cc_start: 0.7531 (t70) cc_final: 0.7257 (t70) REVERT: C 936 ARG cc_start: 0.7287 (ptt90) cc_final: 0.6897 (ppt90) REVERT: C 950 GLU cc_start: 0.8119 (tp30) cc_final: 0.7434 (tp30) REVERT: C 951 MET cc_start: 0.7645 (mtp) cc_final: 0.7128 (mtp) REVERT: C 957 LYS cc_start: 0.8529 (tppt) cc_final: 0.8222 (tppt) REVERT: C 1032 LYS cc_start: 0.8441 (ptpp) cc_final: 0.8170 (pttt) REVERT: C 1033 ARG cc_start: 0.8454 (ttm110) cc_final: 0.7871 (ptm-80) REVERT: C 1064 ASP cc_start: 0.7988 (t0) cc_final: 0.7724 (t70) REVERT: C 1066 MET cc_start: 0.7332 (ttp) cc_final: 0.7091 (ttp) REVERT: C 1131 MET cc_start: 0.7684 (ttm) cc_final: 0.7424 (ttp) REVERT: C 1168 GLU cc_start: 0.7272 (pt0) cc_final: 0.6972 (pm20) REVERT: C 1200 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8150 (ttpp) REVERT: C 1240 ASP cc_start: 0.7962 (p0) cc_final: 0.7617 (p0) REVERT: C 1241 ASP cc_start: 0.7575 (m-30) cc_final: 0.6953 (t0) REVERT: C 1242 LYS cc_start: 0.7887 (mttp) cc_final: 0.7552 (mttm) REVERT: C 1274 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6431 (mm-30) REVERT: C 1304 MET cc_start: 0.7706 (ttp) cc_final: 0.7176 (ttp) REVERT: D 26 SER cc_start: 0.8528 (p) cc_final: 0.8208 (m) REVERT: D 33 TRP cc_start: 0.7087 (m-10) cc_final: 0.6660 (m-10) REVERT: D 101 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.6910 (tpp-160) REVERT: D 117 LEU cc_start: 0.8486 (tp) cc_final: 0.8245 (tt) REVERT: D 130 MET cc_start: 0.7105 (mtt) cc_final: 0.6726 (mtp) REVERT: D 146 VAL cc_start: 0.8325 (t) cc_final: 0.7965 (p) REVERT: D 162 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7466 (mm-30) REVERT: D 176 PHE cc_start: 0.7380 (p90) cc_final: 0.7038 (p90) REVERT: D 192 MET cc_start: 0.7963 (ttp) cc_final: 0.7274 (tmm) REVERT: D 200 GLN cc_start: 0.7853 (pp30) cc_final: 0.7537 (pp30) REVERT: D 204 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 222 LYS cc_start: 0.8149 (tmtt) cc_final: 0.7824 (tttm) REVERT: D 298 MET cc_start: 0.6879 (mmm) cc_final: 0.6563 (mmm) REVERT: D 399 LYS cc_start: 0.8133 (tmmt) cc_final: 0.7493 (tmmt) REVERT: D 534 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6337 (tm-30) REVERT: D 538 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7774 (tpp80) REVERT: D 556 GLU cc_start: 0.7035 (pm20) cc_final: 0.6785 (pm20) REVERT: D 591 ILE cc_start: 0.8099 (tp) cc_final: 0.7725 (tp) REVERT: D 663 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7596 (pp20) REVERT: D 695 LYS cc_start: 0.8369 (tmmt) cc_final: 0.7822 (tmmt) REVERT: D 698 MET cc_start: 0.7992 (tpp) cc_final: 0.7636 (mmm) REVERT: D 715 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7871 (mtmt) REVERT: D 802 ASP cc_start: 0.7230 (t0) cc_final: 0.6984 (t0) REVERT: D 805 GLN cc_start: 0.7691 (pp30) cc_final: 0.7444 (pp30) REVERT: D 821 MET cc_start: 0.7051 (mmp) cc_final: 0.6630 (mmp) REVERT: D 867 GLN cc_start: 0.7261 (tm-30) cc_final: 0.7060 (tm-30) REVERT: D 871 LEU cc_start: 0.8106 (tp) cc_final: 0.7858 (tt) REVERT: D 913 GLU cc_start: 0.7312 (pp20) cc_final: 0.6978 (pp20) REVERT: D 951 GLN cc_start: 0.7810 (tp40) cc_final: 0.7572 (tp40) REVERT: D 992 LYS cc_start: 0.7537 (mptt) cc_final: 0.7296 (mmtt) REVERT: D 1192 LYS cc_start: 0.6788 (mmtm) cc_final: 0.6327 (mmtm) REVERT: D 1261 LEU cc_start: 0.8320 (pp) cc_final: 0.7883 (pp) REVERT: E 53 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7620 (tp30) REVERT: G 11 VAL cc_start: 0.8701 (t) cc_final: 0.8475 (p) REVERT: G 43 MET cc_start: 0.6903 (ppp) cc_final: 0.6242 (ppp) REVERT: G 75 MET cc_start: 0.7498 (mtm) cc_final: 0.6570 (mtm) REVERT: G 76 ASN cc_start: 0.7975 (m-40) cc_final: 0.6798 (p0) REVERT: G 82 LEU cc_start: 0.7231 (mt) cc_final: 0.6971 (mt) outliers start: 33 outliers final: 25 residues processed: 687 average time/residue: 0.4616 time to fit residues: 472.1682 Evaluate side-chains 672 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 647 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 304 optimal weight: 0.4980 chunk 329 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 GLN C 613 ASN C1017 GLN D 504 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28008 Z= 0.187 Angle : 0.551 7.861 38141 Z= 0.289 Chirality : 0.042 0.197 4351 Planarity : 0.004 0.070 4731 Dihedral : 14.891 175.139 4488 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 1.84 % Allowed : 15.93 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3285 helix: 1.26 (0.16), residues: 1084 sheet: 0.01 (0.27), residues: 361 loop : -1.30 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 997 HIS 0.005 0.001 HIS D 545 PHE 0.035 0.001 PHE C 38 TYR 0.028 0.001 TYR D1232 ARG 0.007 0.000 ARG D1222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 672 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.6977 (mpp80) cc_final: 0.5884 (mtm-85) REVERT: A 204 GLU cc_start: 0.7442 (pp20) cc_final: 0.7078 (pp20) REVERT: A 215 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7018 (mm-30) REVERT: B 58 GLU cc_start: 0.7440 (pt0) cc_final: 0.7029 (mm-30) REVERT: B 66 HIS cc_start: 0.7731 (t70) cc_final: 0.7425 (t70) REVERT: B 76 GLU cc_start: 0.6458 (pm20) cc_final: 0.6216 (pm20) REVERT: B 96 ASP cc_start: 0.6571 (t70) cc_final: 0.6263 (t70) REVERT: B 171 LEU cc_start: 0.8047 (mp) cc_final: 0.7202 (tp) REVERT: B 174 ASP cc_start: 0.7599 (m-30) cc_final: 0.7295 (m-30) REVERT: B 181 GLU cc_start: 0.6933 (pm20) cc_final: 0.6540 (pm20) REVERT: B 188 GLU cc_start: 0.7339 (pt0) cc_final: 0.7073 (pt0) REVERT: B 200 LYS cc_start: 0.8462 (tttm) cc_final: 0.8006 (tttm) REVERT: B 227 GLN cc_start: 0.7756 (tp40) cc_final: 0.7457 (tp40) REVERT: C 14 ASP cc_start: 0.7139 (t0) cc_final: 0.6681 (t0) REVERT: C 36 GLN cc_start: 0.7918 (tp40) cc_final: 0.6660 (tm-30) REVERT: C 38 PHE cc_start: 0.7873 (t80) cc_final: 0.7613 (t80) REVERT: C 101 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6830 (ttm-80) REVERT: C 124 MET cc_start: 0.6660 (ptm) cc_final: 0.6259 (ppp) REVERT: C 160 ASP cc_start: 0.7000 (t70) cc_final: 0.6418 (t0) REVERT: C 180 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7676 (tmm-80) REVERT: C 196 VAL cc_start: 0.7523 (t) cc_final: 0.7261 (p) REVERT: C 199 ASP cc_start: 0.6899 (t0) cc_final: 0.6693 (t0) REVERT: C 234 ASP cc_start: 0.8353 (p0) cc_final: 0.8072 (p0) REVERT: C 337 PHE cc_start: 0.6976 (t80) cc_final: 0.6352 (t80) REVERT: C 386 GLU cc_start: 0.7505 (tp30) cc_final: 0.7303 (tp30) REVERT: C 429 MET cc_start: 0.7422 (tpp) cc_final: 0.6965 (tpt) REVERT: C 441 GLU cc_start: 0.6994 (tp30) cc_final: 0.6751 (tp30) REVERT: C 478 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7580 (tpt90) REVERT: C 481 LEU cc_start: 0.7413 (mt) cc_final: 0.6814 (tt) REVERT: C 488 MET cc_start: 0.6920 (mpp) cc_final: 0.6450 (mpp) REVERT: C 514 PHE cc_start: 0.7707 (t80) cc_final: 0.7266 (t80) REVERT: C 568 ASN cc_start: 0.8312 (p0) cc_final: 0.7851 (p0) REVERT: C 592 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8230 (mtp180) REVERT: C 636 CYS cc_start: 0.7776 (m) cc_final: 0.7412 (m) REVERT: C 641 GLU cc_start: 0.6787 (pp20) cc_final: 0.6342 (pp20) REVERT: C 704 MET cc_start: 0.7518 (ppp) cc_final: 0.7051 (ptm) REVERT: C 711 ASP cc_start: 0.7062 (t0) cc_final: 0.6418 (t0) REVERT: C 717 VAL cc_start: 0.8324 (p) cc_final: 0.8036 (t) REVERT: C 719 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7540 (mtmm) REVERT: C 720 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7828 (mtp85) REVERT: C 800 MET cc_start: 0.7998 (pmm) cc_final: 0.7307 (ptp) REVERT: C 848 GLU cc_start: 0.6375 (pt0) cc_final: 0.6035 (pt0) REVERT: C 884 VAL cc_start: 0.6739 (OUTLIER) cc_final: 0.6500 (p) REVERT: C 914 LYS cc_start: 0.7003 (ptmm) cc_final: 0.6756 (ptmm) REVERT: C 930 ASP cc_start: 0.7519 (t70) cc_final: 0.7228 (t70) REVERT: C 936 ARG cc_start: 0.7335 (ptt90) cc_final: 0.6945 (ppt90) REVERT: C 950 GLU cc_start: 0.8134 (tp30) cc_final: 0.7445 (tp30) REVERT: C 951 MET cc_start: 0.7677 (mtp) cc_final: 0.7151 (mtp) REVERT: C 957 LYS cc_start: 0.8538 (tppt) cc_final: 0.8230 (tppt) REVERT: C 1032 LYS cc_start: 0.8446 (ptpp) cc_final: 0.8165 (pttt) REVERT: C 1033 ARG cc_start: 0.8478 (ttm110) cc_final: 0.7866 (ptm-80) REVERT: C 1064 ASP cc_start: 0.7951 (t0) cc_final: 0.7650 (t70) REVERT: C 1066 MET cc_start: 0.7362 (ttp) cc_final: 0.7111 (mtm) REVERT: C 1131 MET cc_start: 0.7704 (ttm) cc_final: 0.7431 (ttp) REVERT: C 1200 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8137 (ttpp) REVERT: C 1229 TYR cc_start: 0.7106 (m-80) cc_final: 0.6695 (m-80) REVERT: C 1240 ASP cc_start: 0.8001 (p0) cc_final: 0.7694 (p0) REVERT: C 1241 ASP cc_start: 0.7646 (m-30) cc_final: 0.6977 (t0) REVERT: C 1304 MET cc_start: 0.7755 (ttp) cc_final: 0.7437 (ttt) REVERT: C 1329 GLU cc_start: 0.7360 (tp30) cc_final: 0.7136 (tp30) REVERT: D 26 SER cc_start: 0.8546 (p) cc_final: 0.8255 (m) REVERT: D 33 TRP cc_start: 0.7244 (m-10) cc_final: 0.6946 (m-10) REVERT: D 60 ARG cc_start: 0.6744 (ttm-80) cc_final: 0.6468 (ttm-80) REVERT: D 117 LEU cc_start: 0.8511 (tp) cc_final: 0.8294 (tt) REVERT: D 130 MET cc_start: 0.7096 (mtt) cc_final: 0.6738 (mtp) REVERT: D 162 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 176 PHE cc_start: 0.7381 (p90) cc_final: 0.6935 (p90) REVERT: D 190 LYS cc_start: 0.8099 (tppp) cc_final: 0.7823 (tptm) REVERT: D 192 MET cc_start: 0.8000 (ttp) cc_final: 0.7239 (tmm) REVERT: D 200 GLN cc_start: 0.7871 (pp30) cc_final: 0.7559 (pp30) REVERT: D 222 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7711 (tttm) REVERT: D 235 GLU cc_start: 0.7688 (pt0) cc_final: 0.7114 (pt0) REVERT: D 280 LYS cc_start: 0.8411 (tptp) cc_final: 0.8168 (tppp) REVERT: D 285 LEU cc_start: 0.8763 (mt) cc_final: 0.8458 (mp) REVERT: D 322 ARG cc_start: 0.7373 (pmt170) cc_final: 0.6891 (pmt170) REVERT: D 556 GLU cc_start: 0.7191 (pm20) cc_final: 0.6827 (pm20) REVERT: D 591 ILE cc_start: 0.8057 (tp) cc_final: 0.7853 (tp) REVERT: D 652 GLU cc_start: 0.7913 (mp0) cc_final: 0.7691 (mp0) REVERT: D 663 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7573 (pp20) REVERT: D 695 LYS cc_start: 0.8421 (tmmt) cc_final: 0.7864 (tmmt) REVERT: D 698 MET cc_start: 0.7936 (tpp) cc_final: 0.7633 (mmm) REVERT: D 715 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7812 (mtmt) REVERT: D 802 ASP cc_start: 0.7377 (t0) cc_final: 0.7066 (t0) REVERT: D 805 GLN cc_start: 0.7810 (pp30) cc_final: 0.7515 (pp30) REVERT: D 822 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6066 (tpp) REVERT: D 867 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7137 (tm-30) REVERT: D 871 LEU cc_start: 0.8075 (tp) cc_final: 0.7813 (tt) REVERT: D 873 GLU cc_start: 0.7943 (tt0) cc_final: 0.7413 (tm-30) REVERT: D 875 ASN cc_start: 0.7861 (m-40) cc_final: 0.7594 (m-40) REVERT: D 992 LYS cc_start: 0.7643 (mptt) cc_final: 0.7436 (mmtt) REVERT: D 1146 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7225 (tp30) REVERT: D 1192 LYS cc_start: 0.6758 (mmtm) cc_final: 0.6486 (mmtt) REVERT: D 1261 LEU cc_start: 0.8225 (pp) cc_final: 0.7739 (pp) REVERT: E 53 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7643 (tp30) REVERT: G 43 MET cc_start: 0.6938 (ppp) cc_final: 0.6288 (ppp) REVERT: G 75 MET cc_start: 0.7403 (mtm) cc_final: 0.6419 (mtm) REVERT: G 76 ASN cc_start: 0.8098 (m-40) cc_final: 0.6937 (p0) REVERT: G 84 ARG cc_start: 0.7729 (ttm170) cc_final: 0.7474 (ttm110) outliers start: 52 outliers final: 39 residues processed: 689 average time/residue: 0.4759 time to fit residues: 486.1082 Evaluate side-chains 696 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 655 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1214 ASP Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 305 optimal weight: 0.6980 chunk 323 optimal weight: 0.0770 chunk 159 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS C 613 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1099 ASN D 504 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28008 Z= 0.163 Angle : 0.542 7.993 38141 Z= 0.282 Chirality : 0.041 0.198 4351 Planarity : 0.004 0.068 4731 Dihedral : 14.905 175.903 4488 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 2.45 % Allowed : 17.84 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3285 helix: 1.34 (0.16), residues: 1079 sheet: 0.02 (0.27), residues: 361 loop : -1.30 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1193 HIS 0.004 0.001 HIS D1218 PHE 0.026 0.001 PHE C 38 TYR 0.033 0.001 TYR D1186 ARG 0.009 0.000 ARG D1222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 657 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7419 (pp20) cc_final: 0.7059 (pp20) REVERT: A 215 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7014 (mm-30) REVERT: B 58 GLU cc_start: 0.7457 (pt0) cc_final: 0.7110 (pt0) REVERT: B 66 HIS cc_start: 0.7778 (t70) cc_final: 0.7325 (t70) REVERT: B 76 GLU cc_start: 0.6334 (pm20) cc_final: 0.6100 (pm20) REVERT: B 96 ASP cc_start: 0.6450 (t70) cc_final: 0.6121 (t70) REVERT: B 143 ARG cc_start: 0.7027 (ptp90) cc_final: 0.6646 (ptp90) REVERT: B 174 ASP cc_start: 0.7611 (m-30) cc_final: 0.7293 (m-30) REVERT: B 188 GLU cc_start: 0.7341 (pt0) cc_final: 0.7068 (pt0) REVERT: B 200 LYS cc_start: 0.8481 (tttm) cc_final: 0.8024 (tttm) REVERT: B 206 GLU cc_start: 0.7170 (tt0) cc_final: 0.6685 (tt0) REVERT: B 227 GLN cc_start: 0.7658 (tp40) cc_final: 0.7393 (tp40) REVERT: C 14 ASP cc_start: 0.7103 (t0) cc_final: 0.6666 (t0) REVERT: C 36 GLN cc_start: 0.7866 (tp40) cc_final: 0.6689 (tm-30) REVERT: C 38 PHE cc_start: 0.7880 (t80) cc_final: 0.7637 (t80) REVERT: C 101 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.7153 (ttm-80) REVERT: C 124 MET cc_start: 0.6615 (ptm) cc_final: 0.6218 (ppp) REVERT: C 126 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6633 (mm-30) REVERT: C 160 ASP cc_start: 0.7067 (t70) cc_final: 0.6487 (t0) REVERT: C 180 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7653 (tmm-80) REVERT: C 199 ASP cc_start: 0.6918 (t0) cc_final: 0.6669 (t0) REVERT: C 234 ASP cc_start: 0.8388 (p0) cc_final: 0.8084 (p0) REVERT: C 337 PHE cc_start: 0.6954 (t80) cc_final: 0.6314 (t80) REVERT: C 429 MET cc_start: 0.7430 (tpp) cc_final: 0.7023 (tpt) REVERT: C 441 GLU cc_start: 0.6990 (tp30) cc_final: 0.6758 (tp30) REVERT: C 481 LEU cc_start: 0.7402 (mt) cc_final: 0.7125 (tt) REVERT: C 488 MET cc_start: 0.6983 (mpp) cc_final: 0.6453 (mpp) REVERT: C 568 ASN cc_start: 0.8337 (p0) cc_final: 0.7889 (p0) REVERT: C 633 LEU cc_start: 0.6825 (mp) cc_final: 0.6195 (tp) REVERT: C 636 CYS cc_start: 0.7824 (m) cc_final: 0.7500 (m) REVERT: C 641 GLU cc_start: 0.6781 (pp20) cc_final: 0.6326 (pp20) REVERT: C 704 MET cc_start: 0.7521 (ppp) cc_final: 0.7083 (ptm) REVERT: C 711 ASP cc_start: 0.6964 (t0) cc_final: 0.6345 (t0) REVERT: C 717 VAL cc_start: 0.8356 (p) cc_final: 0.8055 (t) REVERT: C 719 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7546 (mtmm) REVERT: C 720 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7793 (mtp85) REVERT: C 793 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6541 (mt-10) REVERT: C 800 MET cc_start: 0.7948 (pmm) cc_final: 0.7318 (ptp) REVERT: C 848 GLU cc_start: 0.6371 (pt0) cc_final: 0.6023 (pt0) REVERT: C 884 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6578 (p) REVERT: C 930 ASP cc_start: 0.7521 (t70) cc_final: 0.7240 (t70) REVERT: C 950 GLU cc_start: 0.8138 (tp30) cc_final: 0.7427 (tp30) REVERT: C 951 MET cc_start: 0.7690 (mtp) cc_final: 0.7140 (mtp) REVERT: C 957 LYS cc_start: 0.8509 (tppt) cc_final: 0.8220 (tppt) REVERT: C 1032 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8153 (pttt) REVERT: C 1033 ARG cc_start: 0.8466 (ttm110) cc_final: 0.7855 (ptm-80) REVERT: C 1064 ASP cc_start: 0.7925 (t0) cc_final: 0.7643 (t70) REVERT: C 1066 MET cc_start: 0.7367 (ttp) cc_final: 0.7145 (mtp) REVERT: C 1122 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7787 (ttmt) REVERT: C 1124 ILE cc_start: 0.8249 (mm) cc_final: 0.7969 (mt) REVERT: C 1126 ASP cc_start: 0.6696 (m-30) cc_final: 0.6356 (m-30) REVERT: C 1131 MET cc_start: 0.7703 (ttm) cc_final: 0.7444 (ttp) REVERT: C 1200 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8135 (ttpp) REVERT: C 1240 ASP cc_start: 0.7972 (p0) cc_final: 0.7676 (p0) REVERT: C 1241 ASP cc_start: 0.7597 (m-30) cc_final: 0.6971 (t0) REVERT: C 1304 MET cc_start: 0.7778 (ttp) cc_final: 0.7442 (ttt) REVERT: D 26 SER cc_start: 0.8522 (p) cc_final: 0.8222 (m) REVERT: D 33 TRP cc_start: 0.7289 (m-10) cc_final: 0.6996 (m-10) REVERT: D 60 ARG cc_start: 0.6717 (ttm-80) cc_final: 0.6419 (ttm-80) REVERT: D 96 LYS cc_start: 0.8007 (tppt) cc_final: 0.7589 (tppt) REVERT: D 100 GLU cc_start: 0.6967 (mp0) cc_final: 0.6687 (mp0) REVERT: D 117 LEU cc_start: 0.8478 (tp) cc_final: 0.8239 (tt) REVERT: D 130 MET cc_start: 0.7209 (mtt) cc_final: 0.6877 (mtp) REVERT: D 162 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7590 (mm-30) REVERT: D 176 PHE cc_start: 0.7362 (p90) cc_final: 0.6872 (p90) REVERT: D 190 LYS cc_start: 0.8119 (tppp) cc_final: 0.7887 (tptm) REVERT: D 192 MET cc_start: 0.8007 (ttp) cc_final: 0.7225 (tmm) REVERT: D 219 LYS cc_start: 0.8379 (tmmt) cc_final: 0.8148 (tmmt) REVERT: D 222 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7758 (tttm) REVERT: D 235 GLU cc_start: 0.7722 (pt0) cc_final: 0.7301 (pt0) REVERT: D 280 LYS cc_start: 0.8422 (tptp) cc_final: 0.8120 (tppp) REVERT: D 285 LEU cc_start: 0.8754 (mt) cc_final: 0.8488 (mp) REVERT: D 322 ARG cc_start: 0.7435 (pmt170) cc_final: 0.6837 (pmt170) REVERT: D 416 ILE cc_start: 0.8174 (tt) cc_final: 0.7838 (tt) REVERT: D 556 GLU cc_start: 0.7191 (pm20) cc_final: 0.6807 (pm20) REVERT: D 591 ILE cc_start: 0.8095 (tp) cc_final: 0.7895 (tp) REVERT: D 625 MET cc_start: 0.7188 (tmm) cc_final: 0.6759 (tmm) REVERT: D 643 ASP cc_start: 0.6900 (m-30) cc_final: 0.6629 (m-30) REVERT: D 652 GLU cc_start: 0.7892 (mp0) cc_final: 0.7682 (mp0) REVERT: D 695 LYS cc_start: 0.8425 (tmmt) cc_final: 0.7868 (tmmt) REVERT: D 698 MET cc_start: 0.7931 (tpp) cc_final: 0.7625 (mmm) REVERT: D 715 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7806 (mtmt) REVERT: D 802 ASP cc_start: 0.7415 (t0) cc_final: 0.6799 (t0) REVERT: D 805 GLN cc_start: 0.7819 (pp30) cc_final: 0.7550 (pp30) REVERT: D 822 MET cc_start: 0.6536 (ttm) cc_final: 0.6049 (tpp) REVERT: D 867 GLN cc_start: 0.7387 (tm-30) cc_final: 0.7164 (tm-30) REVERT: D 873 GLU cc_start: 0.7922 (tt0) cc_final: 0.7343 (tm-30) REVERT: D 915 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8088 (pt) REVERT: D 992 LYS cc_start: 0.7703 (mptt) cc_final: 0.7261 (mmtt) REVERT: D 1146 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7085 (tp30) REVERT: D 1261 LEU cc_start: 0.8190 (pp) cc_final: 0.7729 (pp) REVERT: D 1286 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7604 (ttmt) REVERT: D 1325 PHE cc_start: 0.8363 (t80) cc_final: 0.8089 (t80) REVERT: E 53 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7651 (tp30) REVERT: G 43 MET cc_start: 0.6917 (ppp) cc_final: 0.6229 (ppp) REVERT: G 75 MET cc_start: 0.7367 (mtm) cc_final: 0.6400 (mtm) REVERT: G 76 ASN cc_start: 0.8093 (m-40) cc_final: 0.6974 (p0) REVERT: G 82 LEU cc_start: 0.7124 (mt) cc_final: 0.6884 (mt) REVERT: G 84 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7422 (ttm170) outliers start: 69 outliers final: 46 residues processed: 687 average time/residue: 0.4592 time to fit residues: 470.1103 Evaluate side-chains 688 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 640 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1083 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 132 HIS B 23 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN C 41 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 613 ASN C1099 ASN D 504 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1279 GLN D1326 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 28008 Z= 0.487 Angle : 0.723 8.408 38141 Z= 0.384 Chirality : 0.048 0.227 4351 Planarity : 0.005 0.068 4731 Dihedral : 15.244 178.481 4488 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.66 % Rotamer: Outliers : 4.22 % Allowed : 18.23 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3285 helix: 0.70 (0.16), residues: 1076 sheet: -0.25 (0.26), residues: 384 loop : -1.60 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 686 HIS 0.013 0.002 HIS D 545 PHE 0.032 0.003 PHE C 38 TYR 0.034 0.003 TYR D1232 ARG 0.011 0.001 ARG D1222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 704 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8105 (t0) cc_final: 0.7873 (t0) REVERT: A 204 GLU cc_start: 0.7419 (pp20) cc_final: 0.7005 (pp20) REVERT: A 215 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7033 (mm-30) REVERT: B 58 GLU cc_start: 0.7634 (pt0) cc_final: 0.7282 (pt0) REVERT: B 60 GLU cc_start: 0.7746 (tp30) cc_final: 0.7515 (tp30) REVERT: B 61 ILE cc_start: 0.7731 (tp) cc_final: 0.7213 (pt) REVERT: B 66 HIS cc_start: 0.7772 (t70) cc_final: 0.7403 (t70) REVERT: B 96 ASP cc_start: 0.6501 (t70) cc_final: 0.6132 (t70) REVERT: B 174 ASP cc_start: 0.7621 (m-30) cc_final: 0.7208 (m-30) REVERT: B 185 TYR cc_start: 0.8496 (p90) cc_final: 0.8157 (p90) REVERT: B 206 GLU cc_start: 0.6671 (tt0) cc_final: 0.6354 (tt0) REVERT: C 14 ASP cc_start: 0.7391 (t0) cc_final: 0.6871 (t0) REVERT: C 18 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7938 (mmp80) REVERT: C 36 GLN cc_start: 0.8114 (tp40) cc_final: 0.6882 (tm-30) REVERT: C 77 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7367 (mm-30) REVERT: C 124 MET cc_start: 0.7192 (ptm) cc_final: 0.6949 (ptm) REVERT: C 160 ASP cc_start: 0.7269 (t70) cc_final: 0.6648 (t70) REVERT: C 179 TYR cc_start: 0.7398 (t80) cc_final: 0.7193 (t80) REVERT: C 180 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7313 (ttp-170) REVERT: C 199 ASP cc_start: 0.7024 (t0) cc_final: 0.6803 (t0) REVERT: C 211 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7306 (mmt180) REVERT: C 396 ASP cc_start: 0.7208 (p0) cc_final: 0.6581 (p0) REVERT: C 411 ARG cc_start: 0.8313 (tpp80) cc_final: 0.8037 (tpp80) REVERT: C 415 GLU cc_start: 0.7214 (mp0) cc_final: 0.7009 (mp0) REVERT: C 429 MET cc_start: 0.7585 (tpp) cc_final: 0.7178 (tpt) REVERT: C 459 MET cc_start: 0.7666 (mtm) cc_final: 0.7439 (mtt) REVERT: C 461 GLU cc_start: 0.7298 (tt0) cc_final: 0.7072 (tm-30) REVERT: C 503 LYS cc_start: 0.8156 (tppt) cc_final: 0.7877 (mmmm) REVERT: C 592 ARG cc_start: 0.8491 (mtp180) cc_final: 0.8242 (mtp180) REVERT: C 636 CYS cc_start: 0.7752 (m) cc_final: 0.7452 (m) REVERT: C 711 ASP cc_start: 0.7160 (t0) cc_final: 0.6644 (t0) REVERT: C 717 VAL cc_start: 0.8501 (p) cc_final: 0.8207 (t) REVERT: C 719 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7603 (mtmm) REVERT: C 793 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6542 (mt-10) REVERT: C 848 GLU cc_start: 0.6359 (pt0) cc_final: 0.6011 (pt0) REVERT: C 930 ASP cc_start: 0.7445 (t70) cc_final: 0.7166 (t70) REVERT: C 950 GLU cc_start: 0.8200 (tp30) cc_final: 0.7520 (tp30) REVERT: C 951 MET cc_start: 0.7747 (mtp) cc_final: 0.7221 (mtp) REVERT: C 957 LYS cc_start: 0.8518 (tppt) cc_final: 0.8297 (tppt) REVERT: C 1064 ASP cc_start: 0.7871 (t0) cc_final: 0.7555 (t70) REVERT: C 1122 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7904 (ttmt) REVERT: C 1126 ASP cc_start: 0.6738 (m-30) cc_final: 0.6334 (m-30) REVERT: C 1131 MET cc_start: 0.7684 (ttm) cc_final: 0.7392 (ttp) REVERT: C 1141 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7459 (tt) REVERT: C 1240 ASP cc_start: 0.7708 (p0) cc_final: 0.7484 (p0) REVERT: C 1241 ASP cc_start: 0.7561 (m-30) cc_final: 0.6993 (t0) REVERT: C 1297 ASP cc_start: 0.7453 (t0) cc_final: 0.6929 (p0) REVERT: C 1304 MET cc_start: 0.7913 (ttp) cc_final: 0.7591 (ttt) REVERT: D 33 TRP cc_start: 0.7790 (m-10) cc_final: 0.7413 (m-10) REVERT: D 60 ARG cc_start: 0.6959 (ttm-80) cc_final: 0.6660 (ttm-80) REVERT: D 67 ASP cc_start: 0.8047 (t70) cc_final: 0.7582 (t70) REVERT: D 68 TYR cc_start: 0.8659 (m-80) cc_final: 0.8445 (m-80) REVERT: D 130 MET cc_start: 0.7434 (mtt) cc_final: 0.7089 (mtp) REVERT: D 162 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7647 (mm-30) REVERT: D 190 LYS cc_start: 0.8337 (tppp) cc_final: 0.7865 (tptm) REVERT: D 192 MET cc_start: 0.7927 (ttp) cc_final: 0.6772 (tmm) REVERT: D 194 LEU cc_start: 0.7670 (mp) cc_final: 0.7266 (mm) REVERT: D 196 GLN cc_start: 0.7550 (mp10) cc_final: 0.7149 (mp10) REVERT: D 216 LYS cc_start: 0.8380 (tttm) cc_final: 0.8130 (tttm) REVERT: D 219 LYS cc_start: 0.8559 (tmmt) cc_final: 0.8290 (tmmt) REVERT: D 222 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7929 (tttm) REVERT: D 271 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7418 (mtp180) REVERT: D 285 LEU cc_start: 0.8828 (mt) cc_final: 0.8601 (mp) REVERT: D 295 GLU cc_start: 0.7260 (tt0) cc_final: 0.6848 (tt0) REVERT: D 357 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8343 (t) REVERT: D 398 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7582 (tppt) REVERT: D 399 LYS cc_start: 0.8380 (tmmt) cc_final: 0.7634 (tmmt) REVERT: D 402 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6883 (tm-30) REVERT: D 497 GLU cc_start: 0.7073 (pp20) cc_final: 0.6745 (pp20) REVERT: D 517 CYS cc_start: 0.7876 (t) cc_final: 0.7418 (t) REVERT: D 532 GLU cc_start: 0.7262 (pp20) cc_final: 0.7017 (pp20) REVERT: D 556 GLU cc_start: 0.7360 (pm20) cc_final: 0.6982 (pm20) REVERT: D 566 LYS cc_start: 0.8177 (ptmt) cc_final: 0.7903 (ptmm) REVERT: D 591 ILE cc_start: 0.8443 (tp) cc_final: 0.8101 (tp) REVERT: D 611 ILE cc_start: 0.8549 (mm) cc_final: 0.8310 (mm) REVERT: D 625 MET cc_start: 0.7122 (tmm) cc_final: 0.6760 (tmm) REVERT: D 648 GLU cc_start: 0.7732 (pm20) cc_final: 0.7468 (pm20) REVERT: D 652 GLU cc_start: 0.7952 (mp0) cc_final: 0.7740 (mp0) REVERT: D 698 MET cc_start: 0.7902 (tpp) cc_final: 0.7292 (tmm) REVERT: D 715 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7812 (mtmt) REVERT: D 802 ASP cc_start: 0.7507 (t0) cc_final: 0.6927 (t0) REVERT: D 822 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6338 (tpp) REVERT: D 867 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7188 (tm-30) REVERT: D 888 CYS cc_start: 0.7570 (t) cc_final: 0.7326 (t) REVERT: D 898 CYS cc_start: 0.6362 (m) cc_final: 0.5907 (m) REVERT: D 915 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8187 (pt) REVERT: D 932 MET cc_start: 0.5655 (ppp) cc_final: 0.5338 (ppp) REVERT: D 992 LYS cc_start: 0.7898 (mptt) cc_final: 0.7605 (mmtt) REVERT: D 1146 GLU cc_start: 0.7539 (tm-30) cc_final: 0.6969 (tp30) REVERT: D 1158 GLU cc_start: 0.7174 (pm20) cc_final: 0.6625 (pp20) REVERT: D 1246 VAL cc_start: 0.8659 (t) cc_final: 0.8237 (p) REVERT: D 1248 ILE cc_start: 0.7791 (mt) cc_final: 0.7578 (mt) REVERT: D 1321 SER cc_start: 0.7816 (m) cc_final: 0.7586 (t) REVERT: D 1325 PHE cc_start: 0.8466 (t80) cc_final: 0.8116 (t80) REVERT: D 1349 GLU cc_start: 0.7120 (pm20) cc_final: 0.6907 (pm20) REVERT: G 76 ASN cc_start: 0.8324 (m-40) cc_final: 0.7768 (m-40) REVERT: G 82 LEU cc_start: 0.7206 (mt) cc_final: 0.6936 (mt) REVERT: G 84 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7462 (ttm170) outliers start: 119 outliers final: 77 residues processed: 759 average time/residue: 0.4597 time to fit residues: 521.8001 Evaluate side-chains 764 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 681 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 398 LYS Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 0.6980 chunk 291 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 324 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 170 optimal weight: 0.3980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 450 ASN C 613 ASN C 673 HIS C 761 GLN C1099 ASN D 341 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1279 GLN D1326 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28008 Z= 0.173 Angle : 0.599 9.371 38141 Z= 0.311 Chirality : 0.042 0.198 4351 Planarity : 0.004 0.069 4731 Dihedral : 15.125 179.615 4488 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 2.80 % Allowed : 22.17 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3285 helix: 0.97 (0.16), residues: 1098 sheet: -0.07 (0.26), residues: 378 loop : -1.51 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D1193 HIS 0.008 0.001 HIS A 23 PHE 0.032 0.001 PHE C 38 TYR 0.018 0.001 TYR B 185 ARG 0.010 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 668 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8018 (p-80) REVERT: A 86 LYS cc_start: 0.8316 (ttpp) cc_final: 0.8084 (ttpp) REVERT: A 204 GLU cc_start: 0.7449 (pp20) cc_final: 0.6961 (pp20) REVERT: A 215 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6959 (mm-30) REVERT: B 58 GLU cc_start: 0.7600 (pt0) cc_final: 0.7247 (pt0) REVERT: B 61 ILE cc_start: 0.7584 (tp) cc_final: 0.6992 (pt) REVERT: B 66 HIS cc_start: 0.7768 (t70) cc_final: 0.7395 (t70) REVERT: B 181 GLU cc_start: 0.7290 (pm20) cc_final: 0.7078 (pm20) REVERT: C 8 LYS cc_start: 0.8451 (tttt) cc_final: 0.8130 (mtpt) REVERT: C 18 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7927 (mmp80) REVERT: C 36 GLN cc_start: 0.7968 (tp40) cc_final: 0.6907 (tm-30) REVERT: C 77 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 124 MET cc_start: 0.7011 (ptm) cc_final: 0.6767 (ptm) REVERT: C 126 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6741 (mp0) REVERT: C 160 ASP cc_start: 0.7214 (t70) cc_final: 0.6589 (t0) REVERT: C 180 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7499 (ttp-170) REVERT: C 199 ASP cc_start: 0.7012 (t0) cc_final: 0.6783 (t0) REVERT: C 211 ARG cc_start: 0.7697 (mmt180) cc_final: 0.7233 (mmt180) REVERT: C 234 ASP cc_start: 0.8382 (p0) cc_final: 0.8162 (p0) REVERT: C 396 ASP cc_start: 0.7109 (p0) cc_final: 0.6893 (p0) REVERT: C 415 GLU cc_start: 0.7228 (mp0) cc_final: 0.6981 (mp0) REVERT: C 429 MET cc_start: 0.7573 (tpp) cc_final: 0.7073 (tpt) REVERT: C 481 LEU cc_start: 0.7278 (mt) cc_final: 0.6739 (tt) REVERT: C 503 LYS cc_start: 0.8073 (tppt) cc_final: 0.7729 (mtpp) REVERT: C 568 ASN cc_start: 0.8348 (p0) cc_final: 0.7905 (p0) REVERT: C 636 CYS cc_start: 0.7761 (m) cc_final: 0.7360 (m) REVERT: C 711 ASP cc_start: 0.7065 (t0) cc_final: 0.6577 (t0) REVERT: C 717 VAL cc_start: 0.8339 (p) cc_final: 0.8009 (t) REVERT: C 719 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7668 (mtmm) REVERT: C 793 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6534 (mt-10) REVERT: C 848 GLU cc_start: 0.6340 (pt0) cc_final: 0.6002 (pt0) REVERT: C 877 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8647 (m) REVERT: C 930 ASP cc_start: 0.7422 (t70) cc_final: 0.7100 (t70) REVERT: C 950 GLU cc_start: 0.8155 (tp30) cc_final: 0.7453 (tp30) REVERT: C 951 MET cc_start: 0.7662 (mtp) cc_final: 0.7123 (mtp) REVERT: C 957 LYS cc_start: 0.8502 (tppt) cc_final: 0.8256 (tppt) REVERT: C 1030 GLU cc_start: 0.8085 (tp30) cc_final: 0.7167 (tp30) REVERT: C 1122 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7849 (ttmt) REVERT: C 1126 ASP cc_start: 0.6732 (m-30) cc_final: 0.6293 (m-30) REVERT: C 1231 TYR cc_start: 0.8367 (t80) cc_final: 0.8159 (t80) REVERT: C 1240 ASP cc_start: 0.7818 (p0) cc_final: 0.7420 (p0) REVERT: C 1241 ASP cc_start: 0.7538 (m-30) cc_final: 0.6922 (t0) REVERT: C 1273 MET cc_start: 0.7515 (mtm) cc_final: 0.7150 (mtt) REVERT: C 1274 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6753 (mm-30) REVERT: C 1297 ASP cc_start: 0.7466 (t0) cc_final: 0.7111 (t0) REVERT: C 1304 MET cc_start: 0.7883 (ttp) cc_final: 0.7526 (ttt) REVERT: D 33 TRP cc_start: 0.7434 (m-10) cc_final: 0.7126 (m-10) REVERT: D 60 ARG cc_start: 0.6712 (ttm-80) cc_final: 0.6369 (ttm-80) REVERT: D 130 MET cc_start: 0.7428 (mtt) cc_final: 0.7123 (mtp) REVERT: D 162 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7588 (mm-30) REVERT: D 176 PHE cc_start: 0.7539 (p90) cc_final: 0.7256 (p90) REVERT: D 190 LYS cc_start: 0.8274 (tppp) cc_final: 0.7843 (tptm) REVERT: D 192 MET cc_start: 0.7914 (ttp) cc_final: 0.6930 (tmm) REVERT: D 193 ASP cc_start: 0.7045 (t0) cc_final: 0.6668 (t0) REVERT: D 213 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8124 (mmmm) REVERT: D 216 LYS cc_start: 0.8132 (tttm) cc_final: 0.7644 (tttm) REVERT: D 219 LYS cc_start: 0.8505 (tmmt) cc_final: 0.8247 (tmmt) REVERT: D 222 LYS cc_start: 0.8129 (tmtt) cc_final: 0.7856 (tttm) REVERT: D 280 LYS cc_start: 0.8377 (tptp) cc_final: 0.8155 (tppp) REVERT: D 285 LEU cc_start: 0.8797 (mt) cc_final: 0.8542 (mp) REVERT: D 295 GLU cc_start: 0.7185 (tt0) cc_final: 0.6815 (tt0) REVERT: D 402 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6826 (tm-30) REVERT: D 416 ILE cc_start: 0.8131 (tt) cc_final: 0.7815 (tt) REVERT: D 497 GLU cc_start: 0.7106 (pp20) cc_final: 0.6733 (pp20) REVERT: D 532 GLU cc_start: 0.7201 (pp20) cc_final: 0.6980 (pp20) REVERT: D 556 GLU cc_start: 0.7289 (pm20) cc_final: 0.6849 (pm20) REVERT: D 566 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7772 (ptmm) REVERT: D 591 ILE cc_start: 0.8201 (tp) cc_final: 0.7946 (tp) REVERT: D 619 ILE cc_start: 0.8012 (mm) cc_final: 0.7747 (mt) REVERT: D 625 MET cc_start: 0.7120 (tmm) cc_final: 0.6820 (tmm) REVERT: D 652 GLU cc_start: 0.7890 (mp0) cc_final: 0.7689 (mp0) REVERT: D 695 LYS cc_start: 0.8462 (tmmt) cc_final: 0.7882 (tmmt) REVERT: D 698 MET cc_start: 0.7907 (tpp) cc_final: 0.7220 (tmm) REVERT: D 802 ASP cc_start: 0.7435 (t0) cc_final: 0.6929 (t0) REVERT: D 822 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6115 (tpp) REVERT: D 867 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 873 GLU cc_start: 0.7987 (tt0) cc_final: 0.7419 (tm-30) REVERT: D 992 LYS cc_start: 0.7828 (mptt) cc_final: 0.7405 (mmtt) REVERT: D 1029 THR cc_start: 0.5401 (OUTLIER) cc_final: 0.5142 (m) REVERT: D 1146 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6984 (tp30) REVERT: D 1158 GLU cc_start: 0.7208 (pm20) cc_final: 0.6644 (pp20) REVERT: D 1236 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6596 (mp0) REVERT: D 1244 GLN cc_start: 0.7905 (tp40) cc_final: 0.7686 (mm-40) REVERT: D 1259 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7432 (mm-40) REVERT: D 1261 LEU cc_start: 0.8184 (pp) cc_final: 0.7648 (pp) REVERT: E 53 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7536 (tp30) REVERT: G 84 ARG cc_start: 0.7599 (ttm170) cc_final: 0.7395 (ttm110) outliers start: 79 outliers final: 55 residues processed: 706 average time/residue: 0.4559 time to fit residues: 478.0524 Evaluate side-chains 714 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 654 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 184 optimal weight: 0.4980 chunk 236 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 202 optimal weight: 0.0770 chunk 196 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 618 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28008 Z= 0.178 Angle : 0.584 9.442 38141 Z= 0.301 Chirality : 0.042 0.199 4351 Planarity : 0.004 0.069 4731 Dihedral : 15.062 178.141 4488 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 3.12 % Allowed : 22.56 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3285 helix: 1.11 (0.16), residues: 1092 sheet: -0.03 (0.27), residues: 365 loop : -1.49 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.004 0.001 HIS D 545 PHE 0.035 0.001 PHE C 38 TYR 0.018 0.001 TYR B 185 ARG 0.011 0.000 ARG D1222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 660 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8082 (ttpp) REVERT: A 204 GLU cc_start: 0.7517 (pp20) cc_final: 0.7027 (pp20) REVERT: B 58 GLU cc_start: 0.7555 (pt0) cc_final: 0.7238 (pt0) REVERT: B 61 ILE cc_start: 0.7582 (tp) cc_final: 0.7060 (pt) REVERT: B 66 HIS cc_start: 0.7777 (t70) cc_final: 0.7392 (t70) REVERT: B 80 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: B 181 GLU cc_start: 0.7257 (pm20) cc_final: 0.6788 (pm20) REVERT: C 8 LYS cc_start: 0.8543 (tttt) cc_final: 0.8200 (mtpt) REVERT: C 18 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7926 (mmp80) REVERT: C 36 GLN cc_start: 0.7941 (tp40) cc_final: 0.6929 (tm-30) REVERT: C 77 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 124 MET cc_start: 0.6999 (ptm) cc_final: 0.6793 (ptm) REVERT: C 160 ASP cc_start: 0.7247 (t70) cc_final: 0.6625 (t0) REVERT: C 180 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7403 (ttp-170) REVERT: C 199 ASP cc_start: 0.7015 (t0) cc_final: 0.6754 (t0) REVERT: C 211 ARG cc_start: 0.7672 (mmt180) cc_final: 0.7179 (mmt180) REVERT: C 415 GLU cc_start: 0.7229 (mp0) cc_final: 0.6974 (mp0) REVERT: C 429 MET cc_start: 0.7555 (tpp) cc_final: 0.7069 (tpt) REVERT: C 481 LEU cc_start: 0.7173 (mt) cc_final: 0.6896 (tt) REVERT: C 503 LYS cc_start: 0.8126 (tppt) cc_final: 0.7733 (mtpp) REVERT: C 568 ASN cc_start: 0.8324 (p0) cc_final: 0.7872 (p0) REVERT: C 636 CYS cc_start: 0.7726 (m) cc_final: 0.7345 (m) REVERT: C 711 ASP cc_start: 0.7022 (t0) cc_final: 0.6551 (t0) REVERT: C 717 VAL cc_start: 0.8326 (p) cc_final: 0.8001 (t) REVERT: C 719 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7677 (mtmm) REVERT: C 793 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6556 (mt-10) REVERT: C 848 GLU cc_start: 0.6340 (pt0) cc_final: 0.5993 (pt0) REVERT: C 877 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8626 (m) REVERT: C 930 ASP cc_start: 0.7457 (t70) cc_final: 0.7133 (t70) REVERT: C 950 GLU cc_start: 0.8155 (tp30) cc_final: 0.7455 (tp30) REVERT: C 951 MET cc_start: 0.7669 (mtp) cc_final: 0.7128 (mtp) REVERT: C 957 LYS cc_start: 0.8487 (tppt) cc_final: 0.8250 (tppt) REVERT: C 1030 GLU cc_start: 0.8100 (tp30) cc_final: 0.7184 (tp30) REVERT: C 1122 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7881 (ttmt) REVERT: C 1126 ASP cc_start: 0.6744 (m-30) cc_final: 0.6304 (m-30) REVERT: C 1220 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7770 (tm-30) REVERT: C 1231 TYR cc_start: 0.8354 (t80) cc_final: 0.8149 (t80) REVERT: C 1240 ASP cc_start: 0.7872 (p0) cc_final: 0.7462 (p0) REVERT: C 1241 ASP cc_start: 0.7503 (m-30) cc_final: 0.6928 (t0) REVERT: C 1273 MET cc_start: 0.7449 (mtm) cc_final: 0.7245 (mtm) REVERT: C 1274 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6785 (mm-30) REVERT: C 1297 ASP cc_start: 0.7459 (t0) cc_final: 0.7114 (t0) REVERT: C 1304 MET cc_start: 0.7833 (ttp) cc_final: 0.7541 (ttt) REVERT: D 33 TRP cc_start: 0.7397 (m-10) cc_final: 0.7117 (m-10) REVERT: D 60 ARG cc_start: 0.6724 (ttm-80) cc_final: 0.6411 (ttm-80) REVERT: D 130 MET cc_start: 0.7411 (mtt) cc_final: 0.7119 (mtp) REVERT: D 162 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7619 (mm-30) REVERT: D 190 LYS cc_start: 0.8269 (tppp) cc_final: 0.7862 (tptm) REVERT: D 192 MET cc_start: 0.7915 (ttp) cc_final: 0.6820 (tmm) REVERT: D 193 ASP cc_start: 0.7031 (t0) cc_final: 0.6579 (t0) REVERT: D 216 LYS cc_start: 0.8146 (tttm) cc_final: 0.7772 (tttm) REVERT: D 219 LYS cc_start: 0.8505 (tmmt) cc_final: 0.8209 (tmmt) REVERT: D 222 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7623 (tmtt) REVERT: D 280 LYS cc_start: 0.8388 (tptp) cc_final: 0.8154 (tppp) REVERT: D 285 LEU cc_start: 0.8758 (mt) cc_final: 0.8503 (mp) REVERT: D 295 GLU cc_start: 0.7160 (tt0) cc_final: 0.6809 (tt0) REVERT: D 357 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8288 (t) REVERT: D 402 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6811 (tm-30) REVERT: D 416 ILE cc_start: 0.8155 (tt) cc_final: 0.7831 (tt) REVERT: D 497 GLU cc_start: 0.7113 (pp20) cc_final: 0.6632 (pp20) REVERT: D 532 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.7003 (pp20) REVERT: D 538 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7643 (tpp80) REVERT: D 556 GLU cc_start: 0.7316 (pm20) cc_final: 0.6885 (pm20) REVERT: D 566 LYS cc_start: 0.8075 (ptmt) cc_final: 0.7814 (ptmm) REVERT: D 591 ILE cc_start: 0.8088 (tp) cc_final: 0.7859 (tp) REVERT: D 625 MET cc_start: 0.7161 (tmm) cc_final: 0.6864 (tmm) REVERT: D 695 LYS cc_start: 0.8442 (tmmt) cc_final: 0.7863 (tmmt) REVERT: D 698 MET cc_start: 0.7943 (tpp) cc_final: 0.7655 (mmm) REVERT: D 802 ASP cc_start: 0.7339 (t0) cc_final: 0.6763 (t0) REVERT: D 822 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6042 (tpp) REVERT: D 867 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 873 GLU cc_start: 0.8002 (tt0) cc_final: 0.7422 (tm-30) REVERT: D 915 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8145 (pt) REVERT: D 992 LYS cc_start: 0.7810 (mptt) cc_final: 0.7561 (mmtt) REVERT: D 1029 THR cc_start: 0.5400 (OUTLIER) cc_final: 0.5124 (m) REVERT: D 1146 GLU cc_start: 0.7509 (tm-30) cc_final: 0.6966 (tp30) REVERT: D 1158 GLU cc_start: 0.7232 (pm20) cc_final: 0.6641 (pp20) REVERT: D 1222 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8272 (ttp-110) REVERT: D 1236 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6596 (mp0) REVERT: D 1261 LEU cc_start: 0.8200 (pp) cc_final: 0.7653 (pp) REVERT: D 1367 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7034 (pp30) REVERT: E 53 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7529 (tp30) REVERT: G 84 ARG cc_start: 0.7637 (ttm170) cc_final: 0.7429 (ttm170) outliers start: 88 outliers final: 61 residues processed: 701 average time/residue: 0.4575 time to fit residues: 477.2472 Evaluate side-chains 713 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 643 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 192 optimal weight: 0.0050 chunk 97 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 253 optimal weight: 0.0010 overall best weight: 0.5002 ------------------------------------------------------------------------------- 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 613 ASN C1111 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 504 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28008 Z= 0.169 Angle : 0.597 11.597 38141 Z= 0.304 Chirality : 0.042 0.199 4351 Planarity : 0.004 0.069 4731 Dihedral : 15.022 178.695 4488 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 2.91 % Allowed : 23.55 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3285 helix: 1.15 (0.16), residues: 1093 sheet: 0.04 (0.27), residues: 361 loop : -1.46 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.003 0.001 HIS D 545 PHE 0.023 0.001 PHE D1325 TYR 0.012 0.001 TYR C1229 ARG 0.009 0.000 ARG D1222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 655 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7478 (pp20) cc_final: 0.6986 (pp20) REVERT: B 32 GLU cc_start: 0.7513 (tp30) cc_final: 0.7277 (tp30) REVERT: B 58 GLU cc_start: 0.7538 (pt0) cc_final: 0.7220 (pt0) REVERT: B 61 ILE cc_start: 0.7582 (tp) cc_final: 0.6993 (pt) REVERT: B 66 HIS cc_start: 0.7791 (t70) cc_final: 0.7450 (t70) REVERT: B 80 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: B 181 GLU cc_start: 0.7200 (pm20) cc_final: 0.6720 (pm20) REVERT: B 185 TYR cc_start: 0.8465 (p90) cc_final: 0.8122 (p90) REVERT: C 8 LYS cc_start: 0.8518 (tttt) cc_final: 0.8207 (mtpt) REVERT: C 18 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7916 (mmp80) REVERT: C 36 GLN cc_start: 0.7919 (tp40) cc_final: 0.6796 (tm-30) REVERT: C 77 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 126 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6410 (mm-30) REVERT: C 160 ASP cc_start: 0.7241 (t70) cc_final: 0.6631 (t0) REVERT: C 180 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7320 (ttp-170) REVERT: C 199 ASP cc_start: 0.7016 (t0) cc_final: 0.6751 (t0) REVERT: C 211 ARG cc_start: 0.7659 (mmt180) cc_final: 0.7150 (mmt180) REVERT: C 219 GLN cc_start: 0.7465 (pm20) cc_final: 0.7192 (pm20) REVERT: C 415 GLU cc_start: 0.7218 (mp0) cc_final: 0.6973 (mp0) REVERT: C 429 MET cc_start: 0.7509 (tpp) cc_final: 0.6972 (tpt) REVERT: C 478 ARG cc_start: 0.7728 (tpt90) cc_final: 0.7528 (tpt90) REVERT: C 481 LEU cc_start: 0.7196 (mt) cc_final: 0.6757 (tt) REVERT: C 503 LYS cc_start: 0.8052 (tppt) cc_final: 0.7662 (mmmm) REVERT: C 568 ASN cc_start: 0.8305 (p0) cc_final: 0.7862 (p0) REVERT: C 636 CYS cc_start: 0.7702 (m) cc_final: 0.7323 (m) REVERT: C 692 THR cc_start: 0.8500 (p) cc_final: 0.7810 (t) REVERT: C 711 ASP cc_start: 0.7001 (t0) cc_final: 0.6553 (t0) REVERT: C 717 VAL cc_start: 0.8300 (p) cc_final: 0.7987 (t) REVERT: C 719 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7674 (mtmm) REVERT: C 793 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6565 (mt-10) REVERT: C 848 GLU cc_start: 0.6348 (pt0) cc_final: 0.6050 (pt0) REVERT: C 877 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8620 (m) REVERT: C 918 LEU cc_start: 0.8361 (tt) cc_final: 0.8138 (tp) REVERT: C 930 ASP cc_start: 0.7555 (t70) cc_final: 0.7237 (t70) REVERT: C 950 GLU cc_start: 0.8182 (tp30) cc_final: 0.7471 (tp30) REVERT: C 951 MET cc_start: 0.7667 (mtp) cc_final: 0.7120 (mtp) REVERT: C 957 LYS cc_start: 0.8494 (tppt) cc_final: 0.8247 (tppt) REVERT: C 1030 GLU cc_start: 0.8091 (tp30) cc_final: 0.7190 (tp30) REVERT: C 1122 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7860 (ttmt) REVERT: C 1126 ASP cc_start: 0.6742 (m-30) cc_final: 0.6295 (m-30) REVERT: C 1220 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7718 (tm-30) REVERT: C 1231 TYR cc_start: 0.8300 (t80) cc_final: 0.8066 (t80) REVERT: C 1240 ASP cc_start: 0.7901 (p0) cc_final: 0.7459 (p0) REVERT: C 1241 ASP cc_start: 0.7492 (m-30) cc_final: 0.6906 (t0) REVERT: C 1273 MET cc_start: 0.7477 (mtm) cc_final: 0.7242 (mtm) REVERT: C 1274 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6690 (mm-30) REVERT: C 1297 ASP cc_start: 0.7472 (t0) cc_final: 0.7089 (t0) REVERT: C 1304 MET cc_start: 0.7824 (ttp) cc_final: 0.7534 (ttt) REVERT: C 1329 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6766 (tp30) REVERT: D 33 TRP cc_start: 0.7342 (m-10) cc_final: 0.7078 (m-10) REVERT: D 100 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7040 (mm-30) REVERT: D 130 MET cc_start: 0.7436 (mtt) cc_final: 0.7136 (mtp) REVERT: D 162 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 190 LYS cc_start: 0.8261 (tppp) cc_final: 0.7916 (tptm) REVERT: D 192 MET cc_start: 0.7913 (ttp) cc_final: 0.6825 (tmm) REVERT: D 193 ASP cc_start: 0.6998 (t0) cc_final: 0.6585 (t0) REVERT: D 216 LYS cc_start: 0.8136 (tttm) cc_final: 0.7744 (tttm) REVERT: D 219 LYS cc_start: 0.8519 (tmmt) cc_final: 0.8200 (tmmt) REVERT: D 222 LYS cc_start: 0.8074 (tmtt) cc_final: 0.7595 (tmtt) REVERT: D 280 LYS cc_start: 0.8412 (tptp) cc_final: 0.8082 (tppp) REVERT: D 285 LEU cc_start: 0.8746 (mt) cc_final: 0.8488 (mp) REVERT: D 295 GLU cc_start: 0.7143 (tt0) cc_final: 0.6789 (tt0) REVERT: D 357 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8300 (t) REVERT: D 402 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6795 (tm-30) REVERT: D 416 ILE cc_start: 0.8152 (tt) cc_final: 0.7858 (tt) REVERT: D 497 GLU cc_start: 0.7088 (pp20) cc_final: 0.6604 (pp20) REVERT: D 532 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7019 (pp20) REVERT: D 556 GLU cc_start: 0.7331 (pm20) cc_final: 0.6860 (pm20) REVERT: D 566 LYS cc_start: 0.8086 (ptmt) cc_final: 0.7819 (ptmm) REVERT: D 695 LYS cc_start: 0.8412 (tmmt) cc_final: 0.7882 (tmmt) REVERT: D 715 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7729 (mtmt) REVERT: D 802 ASP cc_start: 0.7250 (t0) cc_final: 0.6674 (t0) REVERT: D 821 MET cc_start: 0.7449 (mmp) cc_final: 0.7242 (mmp) REVERT: D 822 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6073 (tpp) REVERT: D 867 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 873 GLU cc_start: 0.7968 (tt0) cc_final: 0.7408 (tm-30) REVERT: D 954 ASN cc_start: 0.8438 (m110) cc_final: 0.7565 (t0) REVERT: D 992 LYS cc_start: 0.7830 (mptt) cc_final: 0.7580 (mmtt) REVERT: D 996 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7875 (mtpp) REVERT: D 1029 THR cc_start: 0.5358 (OUTLIER) cc_final: 0.5084 (m) REVERT: D 1146 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6938 (tp30) REVERT: D 1158 GLU cc_start: 0.7277 (pm20) cc_final: 0.6709 (pp20) REVERT: D 1222 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8251 (ttp-110) REVERT: D 1236 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6584 (mp0) REVERT: D 1261 LEU cc_start: 0.8183 (pp) cc_final: 0.7603 (pp) REVERT: D 1275 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7396 (tt) REVERT: D 1279 GLN cc_start: 0.7697 (tp40) cc_final: 0.7396 (tm-30) REVERT: D 1343 GLU cc_start: 0.7041 (pm20) cc_final: 0.6709 (pm20) REVERT: E 53 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7547 (mm-30) REVERT: E 59 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7054 (pt) outliers start: 82 outliers final: 61 residues processed: 697 average time/residue: 0.4609 time to fit residues: 481.0279 Evaluate side-chains 720 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 650 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 0.5980 chunk 309 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 271 optimal weight: 0.3980 chunk 284 optimal weight: 0.8980 chunk 299 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN D 341 ASN D 504 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28008 Z= 0.186 Angle : 0.604 10.861 38141 Z= 0.307 Chirality : 0.042 0.200 4351 Planarity : 0.004 0.067 4731 Dihedral : 15.001 178.307 4488 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.22 % Rotamer: Outliers : 2.91 % Allowed : 24.02 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3285 helix: 1.16 (0.16), residues: 1094 sheet: -0.07 (0.26), residues: 388 loop : -1.45 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D1193 HIS 0.004 0.001 HIS D 545 PHE 0.017 0.001 PHE D 892 TYR 0.011 0.001 TYR B 177 ARG 0.009 0.000 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 653 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7471 (pp20) cc_final: 0.6982 (pp20) REVERT: B 58 GLU cc_start: 0.7515 (pt0) cc_final: 0.7222 (pt0) REVERT: B 61 ILE cc_start: 0.7693 (tp) cc_final: 0.7088 (pt) REVERT: B 66 HIS cc_start: 0.7808 (t70) cc_final: 0.7451 (t70) REVERT: B 80 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: B 181 GLU cc_start: 0.7196 (pm20) cc_final: 0.6698 (pm20) REVERT: B 185 TYR cc_start: 0.8459 (p90) cc_final: 0.8156 (p90) REVERT: C 8 LYS cc_start: 0.8515 (tttt) cc_final: 0.8206 (mtpt) REVERT: C 18 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7961 (mmp80) REVERT: C 36 GLN cc_start: 0.7893 (tp40) cc_final: 0.6881 (tm-30) REVERT: C 160 ASP cc_start: 0.7275 (t70) cc_final: 0.6696 (t0) REVERT: C 180 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7308 (ttp-170) REVERT: C 199 ASP cc_start: 0.7021 (t0) cc_final: 0.6766 (t0) REVERT: C 211 ARG cc_start: 0.7669 (mmt180) cc_final: 0.7202 (mmt180) REVERT: C 219 GLN cc_start: 0.7426 (pm20) cc_final: 0.7184 (pm20) REVERT: C 429 MET cc_start: 0.7515 (tpp) cc_final: 0.6994 (tpt) REVERT: C 478 ARG cc_start: 0.7767 (tpt90) cc_final: 0.7557 (tpt90) REVERT: C 481 LEU cc_start: 0.7243 (mt) cc_final: 0.6773 (tt) REVERT: C 503 LYS cc_start: 0.8129 (tppt) cc_final: 0.7729 (mmmm) REVERT: C 568 ASN cc_start: 0.8279 (p0) cc_final: 0.7829 (p0) REVERT: C 636 CYS cc_start: 0.7707 (m) cc_final: 0.7334 (m) REVERT: C 711 ASP cc_start: 0.7009 (t0) cc_final: 0.6562 (t0) REVERT: C 717 VAL cc_start: 0.8304 (p) cc_final: 0.8002 (t) REVERT: C 719 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7629 (mtmm) REVERT: C 793 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6593 (mt-10) REVERT: C 848 GLU cc_start: 0.6361 (pt0) cc_final: 0.6063 (pt0) REVERT: C 877 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8618 (m) REVERT: C 918 LEU cc_start: 0.8366 (tt) cc_final: 0.8145 (tp) REVERT: C 930 ASP cc_start: 0.7555 (t70) cc_final: 0.7229 (t70) REVERT: C 950 GLU cc_start: 0.8188 (tp30) cc_final: 0.7480 (tp30) REVERT: C 951 MET cc_start: 0.7683 (mtp) cc_final: 0.7120 (mtp) REVERT: C 957 LYS cc_start: 0.8495 (tppt) cc_final: 0.8252 (tppt) REVERT: C 1030 GLU cc_start: 0.8110 (tp30) cc_final: 0.7186 (tp30) REVERT: C 1122 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7778 (ttmt) REVERT: C 1126 ASP cc_start: 0.6755 (m-30) cc_final: 0.6287 (m-30) REVERT: C 1220 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 1240 ASP cc_start: 0.7873 (p0) cc_final: 0.7437 (p0) REVERT: C 1241 ASP cc_start: 0.7475 (m-30) cc_final: 0.6923 (t0) REVERT: C 1273 MET cc_start: 0.7515 (mtm) cc_final: 0.7262 (mtm) REVERT: C 1274 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6754 (mm-30) REVERT: C 1297 ASP cc_start: 0.7470 (t0) cc_final: 0.7070 (t0) REVERT: C 1304 MET cc_start: 0.7824 (ttp) cc_final: 0.7564 (ttt) REVERT: C 1329 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6801 (tp30) REVERT: C 1340 GLU cc_start: 0.7180 (tp30) cc_final: 0.6915 (tp30) REVERT: D 33 TRP cc_start: 0.7423 (m-10) cc_final: 0.7153 (m-10) REVERT: D 60 ARG cc_start: 0.6748 (ttm-80) cc_final: 0.6539 (ttm-80) REVERT: D 130 MET cc_start: 0.7488 (mtt) cc_final: 0.7180 (mtp) REVERT: D 162 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 190 LYS cc_start: 0.8273 (tppp) cc_final: 0.7872 (tptm) REVERT: D 192 MET cc_start: 0.7908 (ttp) cc_final: 0.6836 (tmm) REVERT: D 193 ASP cc_start: 0.7003 (t0) cc_final: 0.6622 (t0) REVERT: D 216 LYS cc_start: 0.8149 (tttm) cc_final: 0.7768 (tttm) REVERT: D 219 LYS cc_start: 0.8491 (tmmt) cc_final: 0.8194 (tmmt) REVERT: D 222 LYS cc_start: 0.8092 (tmtt) cc_final: 0.7606 (tmtt) REVERT: D 280 LYS cc_start: 0.8418 (tptp) cc_final: 0.8085 (tppp) REVERT: D 285 LEU cc_start: 0.8742 (mt) cc_final: 0.8503 (mp) REVERT: D 295 GLU cc_start: 0.7171 (tt0) cc_final: 0.6784 (tt0) REVERT: D 357 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8288 (t) REVERT: D 402 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6749 (tm-30) REVERT: D 416 ILE cc_start: 0.8169 (tt) cc_final: 0.7858 (tt) REVERT: D 497 GLU cc_start: 0.7141 (pp20) cc_final: 0.6628 (pp20) REVERT: D 532 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7027 (pp20) REVERT: D 538 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7627 (tpp80) REVERT: D 556 GLU cc_start: 0.7329 (pm20) cc_final: 0.6562 (pm20) REVERT: D 566 LYS cc_start: 0.8119 (ptmt) cc_final: 0.7829 (ptmm) REVERT: D 619 ILE cc_start: 0.7953 (mm) cc_final: 0.7719 (mt) REVERT: D 695 LYS cc_start: 0.8411 (tmmt) cc_final: 0.7962 (tmmt) REVERT: D 715 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7719 (mtmt) REVERT: D 802 ASP cc_start: 0.7248 (t0) cc_final: 0.6866 (t0) REVERT: D 822 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6088 (tpp) REVERT: D 867 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 873 GLU cc_start: 0.7965 (tt0) cc_final: 0.7401 (tm-30) REVERT: D 888 CYS cc_start: 0.7260 (t) cc_final: 0.6647 (t) REVERT: D 954 ASN cc_start: 0.8458 (m110) cc_final: 0.7545 (t0) REVERT: D 992 LYS cc_start: 0.7801 (mptt) cc_final: 0.7546 (mmtt) REVERT: D 1029 THR cc_start: 0.5391 (OUTLIER) cc_final: 0.5119 (m) REVERT: D 1146 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6908 (tp30) REVERT: D 1158 GLU cc_start: 0.7381 (pm20) cc_final: 0.6778 (pp20) REVERT: D 1222 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8242 (ttp-110) REVERT: D 1236 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6585 (mp0) REVERT: D 1261 LEU cc_start: 0.8253 (pp) cc_final: 0.7712 (pp) REVERT: D 1263 LYS cc_start: 0.7521 (mmmm) cc_final: 0.7098 (mmmt) REVERT: D 1275 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7378 (tt) REVERT: D 1343 GLU cc_start: 0.7049 (pm20) cc_final: 0.6713 (pm20) REVERT: E 53 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7538 (mm-30) REVERT: E 59 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7076 (pt) REVERT: G 84 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7423 (ttm170) outliers start: 82 outliers final: 67 residues processed: 695 average time/residue: 0.4834 time to fit residues: 507.5810 Evaluate side-chains 723 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 647 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.0870 chunk 318 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 333 optimal weight: 7.9990 chunk 307 optimal weight: 0.3980 chunk 265 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 205 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 613 ASN D 341 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 0.044 28008 Z= 0.176 Angle : 0.607 11.124 38141 Z= 0.307 Chirality : 0.042 0.200 4351 Planarity : 0.004 0.067 4731 Dihedral : 14.985 179.000 4488 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 2.84 % Allowed : 24.44 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3285 helix: 1.19 (0.16), residues: 1092 sheet: 0.00 (0.27), residues: 366 loop : -1.44 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D1193 HIS 0.004 0.001 HIS D 545 PHE 0.018 0.001 PHE D 892 TYR 0.013 0.001 TYR D 382 ARG 0.010 0.000 ARG C 687 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 655 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7476 (pp20) cc_final: 0.7008 (pp20) REVERT: B 58 GLU cc_start: 0.7512 (pt0) cc_final: 0.7220 (pt0) REVERT: B 61 ILE cc_start: 0.7617 (tp) cc_final: 0.7014 (pt) REVERT: B 66 HIS cc_start: 0.7716 (t70) cc_final: 0.7400 (t70) REVERT: B 80 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: B 181 GLU cc_start: 0.7109 (pm20) cc_final: 0.6587 (pm20) REVERT: B 185 TYR cc_start: 0.8449 (p90) cc_final: 0.8174 (p90) REVERT: C 8 LYS cc_start: 0.8516 (tttt) cc_final: 0.8151 (mtpt) REVERT: C 18 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7989 (mmp80) REVERT: C 36 GLN cc_start: 0.7881 (tp40) cc_final: 0.6829 (tm-30) REVERT: C 126 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6390 (mm-30) REVERT: C 160 ASP cc_start: 0.7274 (t70) cc_final: 0.6658 (t0) REVERT: C 180 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.7298 (ttp-170) REVERT: C 199 ASP cc_start: 0.7017 (t0) cc_final: 0.6759 (t0) REVERT: C 211 ARG cc_start: 0.7656 (mmt180) cc_final: 0.7210 (mmt180) REVERT: C 219 GLN cc_start: 0.7412 (pm20) cc_final: 0.7166 (pm20) REVERT: C 429 MET cc_start: 0.7514 (tpp) cc_final: 0.7013 (tpt) REVERT: C 478 ARG cc_start: 0.7775 (tpt90) cc_final: 0.7567 (tpt90) REVERT: C 481 LEU cc_start: 0.7252 (mt) cc_final: 0.6783 (tt) REVERT: C 503 LYS cc_start: 0.8130 (tppt) cc_final: 0.7730 (mmmm) REVERT: C 568 ASN cc_start: 0.8266 (p0) cc_final: 0.7819 (p0) REVERT: C 636 CYS cc_start: 0.7699 (m) cc_final: 0.7325 (m) REVERT: C 711 ASP cc_start: 0.6995 (t0) cc_final: 0.6553 (t0) REVERT: C 717 VAL cc_start: 0.8285 (p) cc_final: 0.7977 (t) REVERT: C 719 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7654 (mtmm) REVERT: C 793 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6603 (mt-10) REVERT: C 848 GLU cc_start: 0.6356 (pt0) cc_final: 0.6062 (pt0) REVERT: C 877 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8616 (m) REVERT: C 918 LEU cc_start: 0.8346 (tt) cc_final: 0.8106 (tp) REVERT: C 930 ASP cc_start: 0.7556 (t70) cc_final: 0.7237 (t70) REVERT: C 950 GLU cc_start: 0.8186 (tp30) cc_final: 0.7452 (tp30) REVERT: C 951 MET cc_start: 0.7679 (mtp) cc_final: 0.7118 (mtp) REVERT: C 957 LYS cc_start: 0.8493 (tppt) cc_final: 0.8250 (tppt) REVERT: C 1030 GLU cc_start: 0.8105 (tp30) cc_final: 0.7182 (tp30) REVERT: C 1122 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7760 (ttmt) REVERT: C 1126 ASP cc_start: 0.6730 (m-30) cc_final: 0.6274 (m-30) REVERT: C 1220 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 1240 ASP cc_start: 0.7983 (p0) cc_final: 0.7523 (p0) REVERT: C 1241 ASP cc_start: 0.7487 (m-30) cc_final: 0.6927 (t0) REVERT: C 1273 MET cc_start: 0.7498 (mtm) cc_final: 0.7234 (mtm) REVERT: C 1274 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6781 (mm-30) REVERT: C 1297 ASP cc_start: 0.7471 (t0) cc_final: 0.7072 (t0) REVERT: C 1304 MET cc_start: 0.7828 (ttp) cc_final: 0.7574 (ttt) REVERT: D 33 TRP cc_start: 0.7381 (m-10) cc_final: 0.7099 (m-10) REVERT: D 60 ARG cc_start: 0.6731 (ttm-80) cc_final: 0.6514 (ttm-80) REVERT: D 100 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7012 (mm-30) REVERT: D 130 MET cc_start: 0.7484 (mtt) cc_final: 0.7180 (mtp) REVERT: D 146 VAL cc_start: 0.8180 (t) cc_final: 0.7770 (p) REVERT: D 162 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7569 (mm-30) REVERT: D 190 LYS cc_start: 0.8265 (tppp) cc_final: 0.7883 (tptm) REVERT: D 192 MET cc_start: 0.7936 (ttp) cc_final: 0.6872 (tmm) REVERT: D 193 ASP cc_start: 0.7009 (t0) cc_final: 0.6604 (t0) REVERT: D 216 LYS cc_start: 0.8146 (tttm) cc_final: 0.7760 (tttm) REVERT: D 219 LYS cc_start: 0.8505 (tmmt) cc_final: 0.8196 (tmmt) REVERT: D 222 LYS cc_start: 0.8086 (tmtt) cc_final: 0.7589 (tmtt) REVERT: D 280 LYS cc_start: 0.8413 (tptp) cc_final: 0.8085 (tppp) REVERT: D 285 LEU cc_start: 0.8735 (mt) cc_final: 0.8497 (mp) REVERT: D 295 GLU cc_start: 0.7181 (tt0) cc_final: 0.6797 (tt0) REVERT: D 357 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8290 (t) REVERT: D 402 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6716 (tm-30) REVERT: D 405 GLU cc_start: 0.6996 (mp0) cc_final: 0.6710 (mp0) REVERT: D 416 ILE cc_start: 0.8159 (tt) cc_final: 0.7857 (tt) REVERT: D 497 GLU cc_start: 0.7153 (pp20) cc_final: 0.6618 (pp20) REVERT: D 532 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7023 (pp20) REVERT: D 538 ARG cc_start: 0.7956 (tpp80) cc_final: 0.7679 (tpp80) REVERT: D 556 GLU cc_start: 0.7305 (pm20) cc_final: 0.6558 (pm20) REVERT: D 566 LYS cc_start: 0.8110 (ptmt) cc_final: 0.7822 (ptmm) REVERT: D 619 ILE cc_start: 0.7942 (mm) cc_final: 0.7705 (mt) REVERT: D 695 LYS cc_start: 0.8397 (tmmt) cc_final: 0.7991 (tmmt) REVERT: D 715 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7712 (mtmp) REVERT: D 802 ASP cc_start: 0.7315 (t0) cc_final: 0.6844 (t0) REVERT: D 822 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6099 (tpp) REVERT: D 867 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7494 (tm-30) REVERT: D 954 ASN cc_start: 0.8452 (m110) cc_final: 0.7533 (t0) REVERT: D 992 LYS cc_start: 0.7788 (mptt) cc_final: 0.7531 (mmtt) REVERT: D 1029 THR cc_start: 0.5353 (OUTLIER) cc_final: 0.5086 (m) REVERT: D 1158 GLU cc_start: 0.7258 (pm20) cc_final: 0.6652 (pp20) REVERT: D 1222 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8246 (ttp-110) REVERT: D 1236 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6577 (mp0) REVERT: D 1261 LEU cc_start: 0.8264 (pp) cc_final: 0.7724 (pp) REVERT: D 1263 LYS cc_start: 0.7498 (mmmm) cc_final: 0.7076 (mmmt) REVERT: D 1275 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7371 (tt) REVERT: E 53 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7550 (mm-30) REVERT: E 59 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7089 (pt) REVERT: G 84 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7459 (ttm170) outliers start: 80 outliers final: 66 residues processed: 699 average time/residue: 0.4510 time to fit residues: 471.4828 Evaluate side-chains 720 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 645 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 0.6980 chunk 283 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN C 613 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113169 restraints weight = 44601.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116590 restraints weight = 23879.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118918 restraints weight = 15512.683| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28008 Z= 0.229 Angle : 0.619 11.104 38141 Z= 0.315 Chirality : 0.042 0.200 4351 Planarity : 0.004 0.067 4731 Dihedral : 15.002 178.062 4488 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 3.12 % Allowed : 24.16 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3285 helix: 1.12 (0.16), residues: 1092 sheet: -0.04 (0.26), residues: 379 loop : -1.49 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D1193 HIS 0.006 0.001 HIS D 545 PHE 0.025 0.001 PHE D1325 TYR 0.025 0.001 TYR C 70 ARG 0.009 0.000 ARG C 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7769.30 seconds wall clock time: 139 minutes 55.03 seconds (8395.03 seconds total)