Starting phenix.real_space_refine on Tue Feb 20 00:45:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0k_13746/02_2024/7q0k_13746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0k_13746/02_2024/7q0k_13746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0k_13746/02_2024/7q0k_13746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0k_13746/02_2024/7q0k_13746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0k_13746/02_2024/7q0k_13746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0k_13746/02_2024/7q0k_13746.pdb" } resolution = 4.0 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= 0.003 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 69 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16276 2.51 5 N 4658 2.21 5 O 5205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C GLU 562": "OE1" <-> "OE2" Residue "C ASP 711": "OD1" <-> "OD2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "C TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1095": "OD1" <-> "OD2" Residue "C GLU 1272": "OE1" <-> "OE2" Residue "C TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1289": "OE1" <-> "OE2" Residue "C GLU 1321": "OE1" <-> "OE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 925": "OE1" <-> "OE2" Residue "D GLU 1215": "OE1" <-> "OE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" 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: 26317 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 498 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} 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: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1694 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: "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 15793 SG CYS D 70 23.011 52.004 96.115 1.00152.66 S ATOM 15807 SG CYS D 72 22.890 49.845 98.770 1.00157.24 S ATOM 21627 SG CYS D 814 42.733 118.516 89.653 1.00109.56 S ATOM 22192 SG CYS D 888 43.855 114.708 91.007 1.00 99.88 S ATOM 22243 SG CYS D 895 43.075 115.802 87.423 1.00103.42 S ATOM 22264 SG CYS D 898 45.940 116.942 88.854 1.00 98.02 S Time building chain proxies: 13.60, per 1000 atoms: 0.52 Number of scatterers: 26317 At special positions: 0 Unit cell: (133.1, 162.8, 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 106 16.00 P 69 15.00 Mg 1 11.99 O 5205 8.00 N 4658 7.00 C 16276 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: 10.94 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5876 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 44 sheets defined 37.5% alpha, 15.0% beta 33 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 8.56 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.222A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.077A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.950A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.754A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.835A 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 228 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.571A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.028A 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: 4.105A 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 removed outlier: 3.606A pdb=" N ILE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 4.014A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.684A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.694A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.782A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.545A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.570A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 4.020A pdb=" N MET C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 862 Processing helix chain 'C' and resid 898 through 906 removed outlier: 3.612A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 903 " --> pdb=" O GLU C 899 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.673A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.694A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.224A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.672A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.957A 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 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.598A 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 58 through 63 removed outlier: 3.575A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.620A 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 192 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.729A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.747A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.867A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 394 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.277A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.541A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.683A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.843A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.567A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 588 through 592' Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.608A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.550A pdb=" N ASP D 643 " --> pdb=" O GLY D 640 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 640 through 644' Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.965A pdb=" N ARG D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.558A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.744A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.738A 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 929 Processing helix chain 'D' and resid 1068 through 1073 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 4.086A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.497A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.855A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.856A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.744A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 3.796A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 33 removed outlier: 4.145A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.588A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.082A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.681A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.851A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.885A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.048A pdb=" N ARG B 12 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 3.829A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.870A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.084A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.798A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.457A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.524A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.519A pdb=" N ILE C 177 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 228 through 231 removed outlier: 3.663A pdb=" N VAL C 228 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.485A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.862A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.618A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.618A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 617 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.852A pdb=" N ALA C 716 " --> pdb=" O ALA C 784 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 750 removed outlier: 7.236A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.976A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.562A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.757A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.736A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.519A pdb=" N ILE D 447 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.690A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.100A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.587A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.742A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.721A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.392A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 3.596A pdb=" N VAL D1027 " --> pdb=" O ALA D1122 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.627A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE7, first strand: chain 'D' and resid 1188 through 1190 removed outlier: 3.889A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 948 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 11.74 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: 8639 1.34 - 1.46: 3807 1.46 - 1.58: 14084 1.58 - 1.70: 134 1.70 - 1.82: 184 Bond restraints: 26848 Sorted by residual: bond pdb=" CB GLU C 142 " pdb=" CG GLU C 142 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" N MET B 51 " pdb=" CA MET B 51 " ideal model delta sigma weight residual 1.457 1.439 0.018 1.41e-02 5.03e+03 1.59e+00 bond pdb=" CD GLU C 142 " pdb=" OE2 GLU C 142 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.33e+00 bond pdb=" C3' U R 4 " pdb=" O3' U R 4 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.30e+00 bond pdb=" C3' DC N 35 " pdb=" O3' DC N 35 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 26843 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.46: 788 105.46 - 112.59: 14162 112.59 - 119.72: 9221 119.72 - 126.85: 12006 126.85 - 133.98: 379 Bond angle restraints: 36556 Sorted by residual: angle pdb=" C CYS C 85 " pdb=" N GLN C 86 " pdb=" CA GLN C 86 " ideal model delta sigma weight residual 121.14 114.25 6.89 1.75e+00 3.27e-01 1.55e+01 angle pdb=" N GLY C 162 " pdb=" CA GLY C 162 " pdb=" C GLY C 162 " ideal model delta sigma weight residual 113.18 121.89 -8.71 2.37e+00 1.78e-01 1.35e+01 angle pdb=" C GLN E 72 " pdb=" N GLN E 73 " pdb=" CA GLN E 73 " ideal model delta sigma weight residual 122.55 115.79 6.76 2.03e+00 2.43e-01 1.11e+01 angle pdb=" C3' U R 4 " pdb=" O3' U R 4 " pdb=" P C R 5 " ideal model delta sigma weight residual 120.20 125.04 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" CA LEU C 992 " pdb=" CB LEU C 992 " pdb=" CG LEU C 992 " ideal model delta sigma weight residual 116.30 127.53 -11.23 3.50e+00 8.16e-02 1.03e+01 ... (remaining 36551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 15892 34.97 - 69.94: 453 69.94 - 104.90: 33 104.90 - 139.87: 2 139.87 - 174.84: 2 Dihedral angle restraints: 16382 sinusoidal: 7247 harmonic: 9135 Sorted by residual: dihedral pdb=" CA LEU D1344 " pdb=" C LEU D1344 " pdb=" N ARG D1345 " pdb=" CA ARG D1345 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ASP C1150 " pdb=" C ASP C1150 " pdb=" N LEU C1151 " pdb=" CA LEU C1151 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 16379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2840 0.037 - 0.074: 929 0.074 - 0.110: 352 0.110 - 0.147: 59 0.147 - 0.184: 4 Chirality restraints: 4184 Sorted by residual: 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 -2.56 -0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CB THR D 514 " pdb=" CA THR D 514 " pdb=" OG1 THR D 514 " pdb=" CG2 THR D 514 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA GLU D 404 " pdb=" N GLU D 404 " pdb=" C GLU D 404 " pdb=" CB GLU D 404 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 4181 not shown) Planarity restraints: 4544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO D 851 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C1103 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO C1104 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C1104 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1104 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 109 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.06e+00 pdb=" N PRO C 110 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.031 5.00e-02 4.00e+02 ... (remaining 4541 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 204 2.54 - 3.13: 20773 3.13 - 3.72: 41307 3.72 - 4.31: 52243 4.31 - 4.90: 84262 Nonbonded interactions: 198789 Sorted by model distance: nonbonded pdb=" OG1 THR C 135 " pdb=" OE2 GLU C 142 " model vdw 1.955 2.440 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.079 2.310 nonbonded pdb=" OG1 THR B 22 " pdb=" O THR B 207 " model vdw 2.143 2.440 nonbonded pdb=" OD1 ASP C 826 " pdb=" OG1 THR C 829 " model vdw 2.144 2.440 nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 2.152 2.496 ... (remaining 198784 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 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.080 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 80.980 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 : 0.003 0.039 26848 Z= 0.217 Angle : 0.642 11.234 36556 Z= 0.346 Chirality : 0.042 0.184 4184 Planarity : 0.004 0.060 4544 Dihedral : 15.704 174.839 10506 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.99 (0.14), residues: 3164 helix: 0.89 (0.16), residues: 1027 sheet: -0.37 (0.30), residues: 297 loop : -1.70 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 115 HIS 0.005 0.001 HIS D 450 PHE 0.019 0.001 PHE C 337 TYR 0.018 0.001 TYR C 105 ARG 0.013 0.001 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 858 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 35 PHE cc_start: 0.7478 (m-10) cc_final: 0.6674 (m-10) REVERT: A 77 ASP cc_start: 0.7221 (m-30) cc_final: 0.6762 (m-30) REVERT: A 91 ARG cc_start: 0.7421 (ttt180) cc_final: 0.7180 (ttp80) REVERT: A 118 ASP cc_start: 0.7683 (p0) cc_final: 0.6949 (p0) REVERT: A 120 ASP cc_start: 0.8179 (p0) cc_final: 0.7406 (p0) REVERT: A 153 VAL cc_start: 0.8722 (t) cc_final: 0.8428 (p) REVERT: A 222 THR cc_start: 0.7704 (m) cc_final: 0.7436 (p) REVERT: A 229 GLU cc_start: 0.6957 (tt0) cc_final: 0.6703 (tt0) REVERT: A 233 ASP cc_start: 0.7204 (t0) cc_final: 0.6968 (t0) REVERT: B 23 HIS cc_start: 0.7435 (t70) cc_final: 0.7048 (t-90) REVERT: B 41 ASN cc_start: 0.8266 (m-40) cc_final: 0.7920 (m-40) REVERT: B 95 LYS cc_start: 0.8231 (mtpp) cc_final: 0.8013 (mtpp) REVERT: B 142 MET cc_start: 0.6776 (mmm) cc_final: 0.6069 (mmm) REVERT: B 174 ASP cc_start: 0.6899 (m-30) cc_final: 0.6412 (m-30) REVERT: B 177 TYR cc_start: 0.7589 (m-80) cc_final: 0.6696 (m-80) REVERT: B 214 GLU cc_start: 0.8377 (mp0) cc_final: 0.8034 (mm-30) REVERT: B 226 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 8 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7277 (mttt) REVERT: C 14 ASP cc_start: 0.6746 (t0) cc_final: 0.6496 (t0) REVERT: C 70 TYR cc_start: 0.6060 (t80) cc_final: 0.5762 (t80) REVERT: C 93 SER cc_start: 0.8140 (p) cc_final: 0.7543 (p) REVERT: C 130 MET cc_start: 0.7685 (tpp) cc_final: 0.7318 (tpp) REVERT: C 150 HIS cc_start: 0.7980 (p90) cc_final: 0.7672 (p90) REVERT: C 180 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7283 (ttp80) REVERT: C 191 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8390 (mtmm) REVERT: C 218 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 245 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7916 (mpp80) REVERT: C 278 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 279 LYS cc_start: 0.8603 (mptt) cc_final: 0.8297 (ptmm) REVERT: C 300 ASP cc_start: 0.7107 (m-30) cc_final: 0.6814 (m-30) REVERT: C 330 HIS cc_start: 0.6533 (m90) cc_final: 0.5931 (m-70) REVERT: C 392 GLU cc_start: 0.7754 (tp30) cc_final: 0.7274 (tp30) REVERT: C 394 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7547 (ttm110) REVERT: C 422 LYS cc_start: 0.7951 (pttm) cc_final: 0.7745 (pttp) REVERT: C 425 ILE cc_start: 0.8228 (tp) cc_final: 0.7997 (tt) REVERT: C 430 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8076 (ttpp) REVERT: C 447 HIS cc_start: 0.7544 (t-170) cc_final: 0.7209 (t-170) REVERT: C 461 GLU cc_start: 0.7989 (tt0) cc_final: 0.7179 (tm-30) REVERT: C 488 MET cc_start: 0.7330 (mmp) cc_final: 0.7086 (mmp) REVERT: C 491 ASP cc_start: 0.7251 (p0) cc_final: 0.6672 (p0) REVERT: C 510 GLN cc_start: 0.7905 (tt0) cc_final: 0.7303 (tp40) REVERT: C 516 ASP cc_start: 0.6445 (t0) cc_final: 0.6167 (t0) REVERT: C 519 ASN cc_start: 0.8033 (m110) cc_final: 0.7660 (m110) REVERT: C 531 SER cc_start: 0.8316 (t) cc_final: 0.7891 (p) REVERT: C 540 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7774 (mtm110) REVERT: C 541 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 603 ILE cc_start: 0.7936 (mp) cc_final: 0.7671 (mm) REVERT: C 653 MET cc_start: 0.7406 (tpp) cc_final: 0.7170 (tpt) REVERT: C 668 ILE cc_start: 0.8299 (mm) cc_final: 0.7977 (mt) REVERT: C 674 ASP cc_start: 0.8020 (t0) cc_final: 0.7750 (t0) REVERT: C 681 MET cc_start: 0.7287 (tpp) cc_final: 0.6797 (ttm) REVERT: C 711 ASP cc_start: 0.7459 (t0) cc_final: 0.7259 (t0) REVERT: C 719 LYS cc_start: 0.7425 (tptp) cc_final: 0.7097 (mmmt) REVERT: C 737 ASN cc_start: 0.8315 (m-40) cc_final: 0.7540 (m110) REVERT: C 755 LYS cc_start: 0.7362 (mmmt) cc_final: 0.7056 (mmtt) REVERT: C 761 GLN cc_start: 0.7666 (mm110) cc_final: 0.7275 (mp10) REVERT: C 775 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 781 ASP cc_start: 0.6391 (t0) cc_final: 0.6108 (t0) REVERT: C 793 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6553 (mt-10) REVERT: C 820 GLU cc_start: 0.7660 (pt0) cc_final: 0.7452 (pt0) REVERT: C 825 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7445 (mm-30) REVERT: C 853 ASP cc_start: 0.8270 (m-30) cc_final: 0.7501 (p0) REVERT: C 864 LYS cc_start: 0.7243 (mmtp) cc_final: 0.6957 (mmtp) REVERT: C 870 ILE cc_start: 0.7793 (mm) cc_final: 0.7587 (mm) REVERT: C 930 ASP cc_start: 0.7027 (t0) cc_final: 0.6791 (t0) REVERT: C 941 LYS cc_start: 0.8548 (mttt) cc_final: 0.8321 (mttt) REVERT: C 951 MET cc_start: 0.8612 (mtp) cc_final: 0.8237 (mtp) REVERT: C 954 LYS cc_start: 0.8510 (mtmm) cc_final: 0.7435 (ptpt) REVERT: C 955 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7626 (tp-100) REVERT: C 957 LYS cc_start: 0.8964 (pptt) cc_final: 0.8592 (pptt) REVERT: C 1026 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 1030 GLU cc_start: 0.8378 (tp30) cc_final: 0.8082 (tp30) REVERT: C 1059 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7494 (mtp85) REVERT: C 1073 LYS cc_start: 0.7897 (ptpt) cc_final: 0.6875 (ptpt) REVERT: C 1085 MET cc_start: 0.7931 (mmt) cc_final: 0.7617 (mmm) REVERT: C 1088 ASP cc_start: 0.7156 (p0) cc_final: 0.6947 (p0) REVERT: C 1119 MET cc_start: 0.7583 (tpp) cc_final: 0.7348 (tmm) REVERT: C 1122 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7452 (mmmm) REVERT: C 1142 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7799 (mtt-85) REVERT: C 1145 ILE cc_start: 0.7572 (mm) cc_final: 0.7348 (mt) REVERT: C 1177 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7749 (ptm160) REVERT: C 1178 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8097 (mmtt) REVERT: C 1180 MET cc_start: 0.7428 (tpt) cc_final: 0.7076 (tpp) REVERT: C 1220 GLN cc_start: 0.7838 (tt0) cc_final: 0.7051 (tm-30) REVERT: C 1238 LEU cc_start: 0.8358 (mm) cc_final: 0.8023 (mt) REVERT: C 1244 HIS cc_start: 0.7529 (t-170) cc_final: 0.7097 (t-170) REVERT: C 1270 PHE cc_start: 0.7196 (t80) cc_final: 0.6015 (t80) REVERT: C 1273 MET cc_start: 0.7606 (mtm) cc_final: 0.7362 (mtp) REVERT: C 1274 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6958 (tp30) REVERT: C 1287 LEU cc_start: 0.8096 (tt) cc_final: 0.7831 (tp) REVERT: C 1290 MET cc_start: 0.7095 (tmm) cc_final: 0.6558 (tmm) REVERT: C 1304 MET cc_start: 0.7028 (tpp) cc_final: 0.6364 (tpp) REVERT: C 1329 GLU cc_start: 0.7586 (tt0) cc_final: 0.6600 (mt-10) REVERT: C 1332 SER cc_start: 0.7861 (t) cc_final: 0.7593 (p) REVERT: C 1337 ILE cc_start: 0.8184 (tp) cc_final: 0.7833 (tt) REVERT: D 21 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7605 (mmtm) REVERT: D 32 SER cc_start: 0.8703 (m) cc_final: 0.8439 (p) REVERT: D 60 ARG cc_start: 0.7514 (ptm-80) cc_final: 0.7059 (tmm-80) REVERT: D 66 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7893 (mmmm) REVERT: D 69 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6927 (tm-30) REVERT: D 84 ILE cc_start: 0.7605 (pt) cc_final: 0.7325 (mp) REVERT: D 130 MET cc_start: 0.7537 (mmt) cc_final: 0.7315 (mmm) REVERT: D 133 ARG cc_start: 0.7132 (tmt170) cc_final: 0.6883 (ttp80) REVERT: D 163 GLU cc_start: 0.8404 (pm20) cc_final: 0.7958 (pm20) REVERT: D 179 LYS cc_start: 0.8149 (mttt) cc_final: 0.7730 (mttt) REVERT: D 183 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 190 LYS cc_start: 0.7869 (ptpp) cc_final: 0.7198 (ptpp) REVERT: D 200 GLN cc_start: 0.8158 (pp30) cc_final: 0.7691 (pp30) REVERT: D 211 GLU cc_start: 0.8138 (pp20) cc_final: 0.7857 (pp20) REVERT: D 215 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8286 (mmtt) REVERT: D 219 LYS cc_start: 0.8373 (mttt) cc_final: 0.8077 (mttt) REVERT: D 221 ILE cc_start: 0.8610 (tp) cc_final: 0.8393 (tp) REVERT: D 222 LYS cc_start: 0.8155 (mptt) cc_final: 0.7788 (mptt) REVERT: D 225 GLU cc_start: 0.7958 (tp30) cc_final: 0.7752 (tp30) REVERT: D 233 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7764 (mmtm) REVERT: D 237 MET cc_start: 0.7834 (tpp) cc_final: 0.7047 (tpp) REVERT: D 244 VAL cc_start: 0.7991 (m) cc_final: 0.7702 (p) REVERT: D 278 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7838 (ttm-80) REVERT: D 280 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8350 (mmmm) REVERT: D 294 ASN cc_start: 0.8054 (t0) cc_final: 0.7711 (t0) REVERT: D 295 GLU cc_start: 0.7949 (tt0) cc_final: 0.7624 (tt0) REVERT: D 297 ARG cc_start: 0.8396 (tmm-80) cc_final: 0.8043 (tmm-80) REVERT: D 301 GLU cc_start: 0.7895 (tp30) cc_final: 0.7330 (tm-30) REVERT: D 304 ASP cc_start: 0.7031 (m-30) cc_final: 0.6562 (m-30) REVERT: D 330 MET cc_start: 0.7459 (ttt) cc_final: 0.7101 (ttt) REVERT: D 339 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7704 (ptm160) REVERT: D 340 GLN cc_start: 0.6903 (tm-30) cc_final: 0.6507 (tp-100) REVERT: D 341 ASN cc_start: 0.7673 (m-40) cc_final: 0.7346 (t0) REVERT: D 378 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7150 (mtpp) REVERT: D 381 ILE cc_start: 0.8106 (mm) cc_final: 0.7749 (mp) REVERT: D 399 LYS cc_start: 0.8190 (mppt) cc_final: 0.7703 (mmtt) REVERT: D 400 MET cc_start: 0.8072 (mtm) cc_final: 0.7139 (mtt) REVERT: D 402 GLU cc_start: 0.7597 (pp20) cc_final: 0.7285 (pp20) REVERT: D 403 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7687 (ttm110) REVERT: D 405 GLU cc_start: 0.7240 (mp0) cc_final: 0.6775 (mp0) REVERT: D 432 LEU cc_start: 0.8415 (mm) cc_final: 0.8049 (mt) REVERT: D 442 ILE cc_start: 0.8450 (tt) cc_final: 0.8111 (tt) REVERT: D 443 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6714 (mm-30) REVERT: D 454 CYS cc_start: 0.7633 (m) cc_final: 0.7430 (m) REVERT: D 479 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7708 (tm-30) REVERT: D 484 MET cc_start: 0.7456 (mmm) cc_final: 0.7243 (mmm) REVERT: D 485 MET cc_start: 0.7580 (mmt) cc_final: 0.7293 (mmp) REVERT: D 506 VAL cc_start: 0.8165 (m) cc_final: 0.7804 (p) REVERT: D 511 TYR cc_start: 0.7651 (t80) cc_final: 0.7107 (t80) REVERT: D 531 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7929 (ttmm) REVERT: D 536 LEU cc_start: 0.8240 (mt) cc_final: 0.8010 (mt) REVERT: D 547 ARG cc_start: 0.7099 (mpt-90) cc_final: 0.6810 (mmt90) REVERT: D 625 MET cc_start: 0.7959 (tmm) cc_final: 0.7643 (tmm) REVERT: D 644 MET cc_start: 0.8174 (mpp) cc_final: 0.7719 (mtm) REVERT: D 658 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8431 (mm-30) REVERT: D 678 ARG cc_start: 0.8483 (ppt170) cc_final: 0.8230 (ttp80) REVERT: D 715 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7897 (ttpp) REVERT: D 722 ILE cc_start: 0.8473 (tp) cc_final: 0.8190 (tt) REVERT: D 724 MET cc_start: 0.8061 (ttp) cc_final: 0.7553 (ttp) REVERT: D 728 SER cc_start: 0.8479 (p) cc_final: 0.7967 (t) REVERT: D 733 SER cc_start: 0.7908 (t) cc_final: 0.6940 (p) REVERT: D 739 GLN cc_start: 0.7945 (tt0) cc_final: 0.7547 (tt0) REVERT: D 747 MET cc_start: 0.6640 (mmp) cc_final: 0.6167 (mmp) REVERT: D 756 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7245 (mm-30) REVERT: D 757 THR cc_start: 0.8674 (t) cc_final: 0.8473 (m) REVERT: D 780 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7749 (ttm170) REVERT: D 781 LYS cc_start: 0.8658 (tptp) cc_final: 0.8241 (tppt) REVERT: D 808 VAL cc_start: 0.8399 (t) cc_final: 0.7985 (p) REVERT: D 822 MET cc_start: 0.7983 (tpp) cc_final: 0.7671 (tpp) REVERT: D 839 VAL cc_start: 0.8090 (t) cc_final: 0.7824 (p) REVERT: D 860 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7228 (ptm160) REVERT: D 873 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8090 (mt-10) REVERT: D 905 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6773 (mmm-85) REVERT: D 911 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8213 (ttmt) REVERT: D 964 LYS cc_start: 0.8028 (tppt) cc_final: 0.7713 (tppt) REVERT: D 992 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7823 (mmtt) REVERT: D 995 TYR cc_start: 0.7543 (m-80) cc_final: 0.7271 (m-10) REVERT: D 1007 ASP cc_start: 0.8355 (t70) cc_final: 0.8064 (t0) REVERT: D 1020 TRP cc_start: 0.7585 (p-90) cc_final: 0.7061 (p-90) REVERT: D 1119 ASP cc_start: 0.7606 (t0) cc_final: 0.7207 (m-30) REVERT: D 1144 LEU cc_start: 0.8034 (mm) cc_final: 0.6805 (mt) REVERT: D 1146 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 1152 GLU cc_start: 0.7268 (mp0) cc_final: 0.6998 (mp0) REVERT: D 1173 ARG cc_start: 0.7100 (ttp-110) cc_final: 0.6526 (ttp-110) REVERT: D 1188 GLU cc_start: 0.7808 (pm20) cc_final: 0.7295 (pm20) REVERT: D 1189 MET cc_start: 0.7263 (mmp) cc_final: 0.7040 (mmp) REVERT: D 1193 TRP cc_start: 0.7380 (p-90) cc_final: 0.7145 (p-90) REVERT: D 1222 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.8084 (ptm-80) REVERT: D 1223 LEU cc_start: 0.8399 (mm) cc_final: 0.7662 (mm) REVERT: D 1235 ASN cc_start: 0.7580 (m110) cc_final: 0.6913 (m-40) REVERT: D 1236 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6581 (tm-30) REVERT: D 1239 ASP cc_start: 0.7492 (m-30) cc_final: 0.7074 (m-30) REVERT: D 1254 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6491 (tm-30) REVERT: D 1292 LEU cc_start: 0.8482 (tp) cc_final: 0.8207 (tp) REVERT: D 1325 PHE cc_start: 0.6490 (t80) cc_final: 0.6235 (t80) REVERT: D 1334 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7550 (mm-30) REVERT: E 3 ARG cc_start: 0.6738 (mmp-170) cc_final: 0.6505 (mmp-170) REVERT: E 68 GLU cc_start: 0.8190 (tp30) cc_final: 0.7974 (tp30) outliers start: 0 outliers final: 0 residues processed: 858 average time/residue: 0.3961 time to fit residues: 500.0393 Evaluate side-chains 756 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 0.0470 chunk 244 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 292 optimal weight: 0.7980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 760 ASN C 824 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1175 ASN C1244 HIS C1257 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 545 HIS D 665 GLN D 669 GLN D 777 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26848 Z= 0.177 Angle : 0.641 11.672 36556 Z= 0.327 Chirality : 0.043 0.205 4184 Planarity : 0.004 0.060 4544 Dihedral : 14.766 173.157 4287 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.37 % Allowed : 11.82 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 3164 helix: 0.88 (0.16), residues: 1059 sheet: -0.26 (0.28), residues: 326 loop : -1.73 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1193 HIS 0.006 0.001 HIS D 545 PHE 0.016 0.001 PHE C 224 TYR 0.012 0.001 TYR C 105 ARG 0.008 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 804 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6438 (tm-30) REVERT: A 68 TYR cc_start: 0.8413 (m-10) cc_final: 0.8135 (m-10) REVERT: A 77 ASP cc_start: 0.6702 (m-30) cc_final: 0.6309 (m-30) REVERT: A 80 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6722 (tm-30) REVERT: A 118 ASP cc_start: 0.7718 (p0) cc_final: 0.7120 (p0) REVERT: A 120 ASP cc_start: 0.7977 (p0) cc_final: 0.7415 (p0) REVERT: A 153 VAL cc_start: 0.8615 (t) cc_final: 0.8310 (p) REVERT: A 205 MET cc_start: 0.7281 (ttp) cc_final: 0.6968 (ttm) REVERT: A 222 THR cc_start: 0.7610 (m) cc_final: 0.7317 (p) REVERT: A 233 ASP cc_start: 0.7116 (t0) cc_final: 0.6880 (t0) REVERT: B 23 HIS cc_start: 0.7433 (t70) cc_final: 0.7208 (t-90) REVERT: B 41 ASN cc_start: 0.8135 (m-40) cc_final: 0.7895 (m-40) REVERT: B 95 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7984 (mtpp) REVERT: B 140 ILE cc_start: 0.8287 (tp) cc_final: 0.7450 (tp) REVERT: B 142 MET cc_start: 0.6868 (mmm) cc_final: 0.6022 (mmm) REVERT: B 174 ASP cc_start: 0.6963 (m-30) cc_final: 0.6400 (m-30) REVERT: B 177 TYR cc_start: 0.7571 (m-80) cc_final: 0.6643 (m-80) REVERT: B 191 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6650 (ttp80) REVERT: B 214 GLU cc_start: 0.8341 (mp0) cc_final: 0.8058 (mm-30) REVERT: B 226 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 7 GLU cc_start: 0.7042 (mp0) cc_final: 0.6825 (mp0) REVERT: C 8 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7276 (mttt) REVERT: C 99 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7744 (tppt) REVERT: C 130 MET cc_start: 0.7716 (tpp) cc_final: 0.7257 (tpp) REVERT: C 150 HIS cc_start: 0.7908 (p90) cc_final: 0.7680 (p-80) REVERT: C 169 LYS cc_start: 0.8002 (tmtt) cc_final: 0.7709 (tmtt) REVERT: C 191 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8336 (mtmm) REVERT: C 219 GLN cc_start: 0.8458 (mt0) cc_final: 0.8194 (mt0) REVERT: C 283 LYS cc_start: 0.7709 (tppt) cc_final: 0.7331 (tppt) REVERT: C 300 ASP cc_start: 0.6690 (m-30) cc_final: 0.6454 (m-30) REVERT: C 330 HIS cc_start: 0.6613 (m90) cc_final: 0.5973 (m-70) REVERT: C 366 ILE cc_start: 0.8156 (mm) cc_final: 0.7797 (mm) REVERT: C 392 GLU cc_start: 0.7715 (tp30) cc_final: 0.7218 (tp30) REVERT: C 394 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7631 (ttm110) REVERT: C 425 ILE cc_start: 0.8335 (tp) cc_final: 0.7844 (tt) REVERT: C 429 MET cc_start: 0.8304 (mtt) cc_final: 0.7889 (mtm) REVERT: C 430 LYS cc_start: 0.8227 (ttpt) cc_final: 0.8008 (ttpp) REVERT: C 447 HIS cc_start: 0.7552 (t-170) cc_final: 0.7261 (t-170) REVERT: C 461 GLU cc_start: 0.8030 (tt0) cc_final: 0.7161 (tm-30) REVERT: C 524 ILE cc_start: 0.7234 (mm) cc_final: 0.6955 (tp) REVERT: C 531 SER cc_start: 0.8221 (t) cc_final: 0.8007 (t) REVERT: C 540 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8121 (mtm110) REVERT: C 541 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7819 (mm-30) REVERT: C 554 HIS cc_start: 0.7586 (m170) cc_final: 0.7372 (m170) REVERT: C 580 GLN cc_start: 0.7441 (mt0) cc_final: 0.7229 (mt0) REVERT: C 620 ASN cc_start: 0.7915 (p0) cc_final: 0.7711 (p0) REVERT: C 668 ILE cc_start: 0.8186 (mm) cc_final: 0.7965 (mt) REVERT: C 674 ASP cc_start: 0.7785 (t0) cc_final: 0.7498 (t0) REVERT: C 681 MET cc_start: 0.7272 (tpp) cc_final: 0.6496 (ttm) REVERT: C 685 MET cc_start: 0.6948 (mpp) cc_final: 0.5745 (mpp) REVERT: C 719 LYS cc_start: 0.7409 (tptp) cc_final: 0.7108 (mmmt) REVERT: C 737 ASN cc_start: 0.8255 (m-40) cc_final: 0.7520 (m110) REVERT: C 755 LYS cc_start: 0.7164 (mmmt) cc_final: 0.6820 (mmtt) REVERT: C 761 GLN cc_start: 0.7713 (mm110) cc_final: 0.7450 (mp10) REVERT: C 775 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7240 (tm-30) REVERT: C 781 ASP cc_start: 0.6720 (t0) cc_final: 0.6370 (t0) REVERT: C 793 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6446 (mt-10) REVERT: C 800 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7277 (ptm) REVERT: C 811 ASN cc_start: 0.8040 (p0) cc_final: 0.7692 (p0) REVERT: C 825 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7436 (mm-30) REVERT: C 826 ASP cc_start: 0.7094 (t0) cc_final: 0.6882 (t0) REVERT: C 853 ASP cc_start: 0.8239 (m-30) cc_final: 0.7543 (p0) REVERT: C 864 LYS cc_start: 0.7312 (mmtp) cc_final: 0.7076 (mmtp) REVERT: C 930 ASP cc_start: 0.6963 (t0) cc_final: 0.6745 (t0) REVERT: C 951 MET cc_start: 0.8590 (mtp) cc_final: 0.8308 (mtp) REVERT: C 954 LYS cc_start: 0.8585 (mtmm) cc_final: 0.7484 (ptpt) REVERT: C 957 LYS cc_start: 0.8973 (pptt) cc_final: 0.8593 (pptt) REVERT: C 1030 GLU cc_start: 0.8437 (tp30) cc_final: 0.8173 (tp30) REVERT: C 1079 ILE cc_start: 0.8072 (mm) cc_final: 0.7294 (mm) REVERT: C 1119 MET cc_start: 0.7575 (tpp) cc_final: 0.7370 (tmm) REVERT: C 1142 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7694 (mtt-85) REVERT: C 1178 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8117 (mmtt) REVERT: C 1180 MET cc_start: 0.7450 (tpt) cc_final: 0.7206 (tpp) REVERT: C 1200 LYS cc_start: 0.8169 (tptp) cc_final: 0.7877 (tptp) REVERT: C 1216 ARG cc_start: 0.7367 (mtt90) cc_final: 0.7082 (mtt90) REVERT: C 1238 LEU cc_start: 0.8268 (mm) cc_final: 0.8041 (mt) REVERT: C 1268 GLN cc_start: 0.7726 (mp10) cc_final: 0.7329 (mp10) REVERT: C 1270 PHE cc_start: 0.7179 (t80) cc_final: 0.6248 (t80) REVERT: C 1290 MET cc_start: 0.7256 (tmm) cc_final: 0.6881 (tmm) REVERT: C 1315 MET cc_start: 0.7528 (mmm) cc_final: 0.6897 (mmm) REVERT: C 1329 GLU cc_start: 0.7526 (tt0) cc_final: 0.6628 (mt-10) REVERT: C 1337 ILE cc_start: 0.8223 (tp) cc_final: 0.7955 (tt) REVERT: D 21 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7587 (mmmm) REVERT: D 32 SER cc_start: 0.8814 (m) cc_final: 0.8594 (p) REVERT: D 35 PHE cc_start: 0.6965 (m-80) cc_final: 0.6574 (m-80) REVERT: D 42 GLU cc_start: 0.7747 (pm20) cc_final: 0.7514 (pm20) REVERT: D 50 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8694 (tmtt) REVERT: D 60 ARG cc_start: 0.7423 (ptm-80) cc_final: 0.7024 (tmm-80) REVERT: D 66 LYS cc_start: 0.8264 (mmmm) cc_final: 0.8048 (mmmm) REVERT: D 69 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 84 ILE cc_start: 0.7635 (pt) cc_final: 0.7385 (mp) REVERT: D 94 GLN cc_start: 0.6865 (tp40) cc_final: 0.6658 (tp40) REVERT: D 130 MET cc_start: 0.7594 (mmt) cc_final: 0.7313 (mmm) REVERT: D 163 GLU cc_start: 0.8252 (pm20) cc_final: 0.7949 (pm20) REVERT: D 179 LYS cc_start: 0.8376 (mttt) cc_final: 0.7753 (mttt) REVERT: D 183 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 190 LYS cc_start: 0.7830 (ptpp) cc_final: 0.7228 (ptpp) REVERT: D 200 GLN cc_start: 0.8297 (pp30) cc_final: 0.7737 (pp30) REVERT: D 203 GLU cc_start: 0.8596 (pp20) cc_final: 0.8346 (pp20) REVERT: D 211 GLU cc_start: 0.8190 (pp20) cc_final: 0.7692 (pp20) REVERT: D 215 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8284 (mmtm) REVERT: D 219 LYS cc_start: 0.8455 (mttt) cc_final: 0.7921 (mmtp) REVERT: D 222 LYS cc_start: 0.8237 (mptt) cc_final: 0.7796 (mptt) REVERT: D 225 GLU cc_start: 0.7942 (tp30) cc_final: 0.7653 (tp30) REVERT: D 233 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7793 (mmtm) REVERT: D 241 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7821 (p) REVERT: D 278 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7810 (ttm-80) REVERT: D 294 ASN cc_start: 0.8062 (t0) cc_final: 0.7677 (t0) REVERT: D 295 GLU cc_start: 0.7955 (tt0) cc_final: 0.7659 (tt0) REVERT: D 297 ARG cc_start: 0.8367 (tmm-80) cc_final: 0.8082 (tmm-80) REVERT: D 301 GLU cc_start: 0.7832 (tp30) cc_final: 0.7231 (tm-30) REVERT: D 304 ASP cc_start: 0.6886 (m-30) cc_final: 0.6630 (m-30) REVERT: D 330 MET cc_start: 0.7407 (ttt) cc_final: 0.7111 (ttt) REVERT: D 339 ARG cc_start: 0.8024 (ttp-110) cc_final: 0.7369 (ttp-110) REVERT: D 340 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6573 (tp-100) REVERT: D 341 ASN cc_start: 0.7723 (m-40) cc_final: 0.7324 (t0) REVERT: D 370 LYS cc_start: 0.7694 (tttt) cc_final: 0.7321 (tttp) REVERT: D 378 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7147 (mtpp) REVERT: D 382 TYR cc_start: 0.7847 (m-10) cc_final: 0.7088 (m-10) REVERT: D 399 LYS cc_start: 0.8227 (mppt) cc_final: 0.7757 (mppt) REVERT: D 400 MET cc_start: 0.8117 (mtm) cc_final: 0.7090 (mtt) REVERT: D 404 GLU cc_start: 0.7918 (pm20) cc_final: 0.7694 (pm20) REVERT: D 405 GLU cc_start: 0.7246 (mp0) cc_final: 0.6773 (mp0) REVERT: D 417 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7103 (ttp80) REVERT: D 431 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7908 (ttp-110) REVERT: D 432 LEU cc_start: 0.8396 (mm) cc_final: 0.7960 (mm) REVERT: D 438 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6663 (tm-30) REVERT: D 479 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7546 (tm-30) REVERT: D 506 VAL cc_start: 0.8231 (m) cc_final: 0.7885 (p) REVERT: D 511 TYR cc_start: 0.7539 (t80) cc_final: 0.6987 (t80) REVERT: D 531 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7994 (ttmm) REVERT: D 604 MET cc_start: 0.7620 (tmm) cc_final: 0.7170 (tmm) REVERT: D 625 MET cc_start: 0.7832 (tmm) cc_final: 0.7631 (tmm) REVERT: D 644 MET cc_start: 0.8115 (mpp) cc_final: 0.7543 (mtm) REVERT: D 658 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 678 ARG cc_start: 0.8500 (ppt170) cc_final: 0.8235 (ttp80) REVERT: D 715 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7876 (tppt) REVERT: D 722 ILE cc_start: 0.8451 (tp) cc_final: 0.8201 (tt) REVERT: D 724 MET cc_start: 0.7819 (ttp) cc_final: 0.7442 (mtp) REVERT: D 728 SER cc_start: 0.8409 (p) cc_final: 0.7929 (t) REVERT: D 738 ARG cc_start: 0.7611 (ttm110) cc_final: 0.6994 (ttm110) REVERT: D 781 LYS cc_start: 0.8690 (tptp) cc_final: 0.8231 (tppt) REVERT: D 789 LYS cc_start: 0.7899 (ptmm) cc_final: 0.7353 (tttt) REVERT: D 802 ASP cc_start: 0.6947 (p0) cc_final: 0.6712 (p0) REVERT: D 808 VAL cc_start: 0.8425 (t) cc_final: 0.8064 (p) REVERT: D 821 MET cc_start: 0.7432 (tpt) cc_final: 0.6918 (tpt) REVERT: D 850 LYS cc_start: 0.8441 (tmtt) cc_final: 0.8208 (tptt) REVERT: D 860 ARG cc_start: 0.7717 (ptm160) cc_final: 0.7235 (ptm160) REVERT: D 873 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8063 (mt-10) REVERT: D 911 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8332 (ttmt) REVERT: D 921 GLN cc_start: 0.7768 (tt0) cc_final: 0.7323 (tt0) REVERT: D 981 GLU cc_start: 0.7664 (tp30) cc_final: 0.7252 (tp30) REVERT: D 983 LYS cc_start: 0.7367 (mptt) cc_final: 0.6930 (ptpt) REVERT: D 1020 TRP cc_start: 0.7492 (p-90) cc_final: 0.6977 (p-90) REVERT: D 1040 MET cc_start: 0.4437 (OUTLIER) cc_final: 0.3924 (tpp) REVERT: D 1095 MET cc_start: 0.6418 (pmm) cc_final: 0.6178 (pmm) REVERT: D 1119 ASP cc_start: 0.7635 (t0) cc_final: 0.7227 (m-30) REVERT: D 1144 LEU cc_start: 0.8511 (mm) cc_final: 0.8162 (mt) REVERT: D 1146 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7505 (mm-30) REVERT: D 1189 MET cc_start: 0.7212 (mmp) cc_final: 0.6943 (mmp) REVERT: D 1222 ARG cc_start: 0.8447 (ptm-80) cc_final: 0.8182 (ptm-80) REVERT: D 1223 LEU cc_start: 0.8481 (mm) cc_final: 0.7703 (mm) REVERT: D 1247 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7548 (ttmt) REVERT: D 1292 LEU cc_start: 0.8466 (tp) cc_final: 0.8205 (tp) REVERT: D 1325 PHE cc_start: 0.6528 (t80) cc_final: 0.6192 (t80) REVERT: D 1334 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7466 (mm-30) REVERT: D 1342 ASP cc_start: 0.7332 (t0) cc_final: 0.7042 (t0) REVERT: D 1366 HIS cc_start: 0.7806 (m170) cc_final: 0.7258 (m170) REVERT: E 68 GLU cc_start: 0.8182 (tp30) cc_final: 0.7893 (tp30) outliers start: 37 outliers final: 22 residues processed: 812 average time/residue: 0.4511 time to fit residues: 538.0386 Evaluate side-chains 775 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 750 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1367 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 0.0030 chunk 243 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 316 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 290 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 147 GLN B 132 HIS ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS C 628 HIS C 760 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26848 Z= 0.266 Angle : 0.662 11.055 36556 Z= 0.341 Chirality : 0.044 0.200 4184 Planarity : 0.005 0.055 4544 Dihedral : 14.780 174.497 4287 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.25 % Allowed : 15.36 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.04 (0.14), residues: 3164 helix: 0.70 (0.16), residues: 1065 sheet: -0.37 (0.28), residues: 343 loop : -1.72 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 33 HIS 0.015 0.001 HIS C1023 PHE 0.027 0.002 PHE C1025 TYR 0.018 0.002 TYR D 140 ARG 0.014 0.001 ARG D 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 785 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7980 (mtpp) REVERT: A 67 GLU cc_start: 0.7813 (tp30) cc_final: 0.7487 (tp30) REVERT: A 77 ASP cc_start: 0.6738 (m-30) cc_final: 0.6481 (m-30) REVERT: A 80 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6843 (tm-30) REVERT: A 118 ASP cc_start: 0.7866 (p0) cc_final: 0.7334 (p0) REVERT: A 120 ASP cc_start: 0.7910 (p0) cc_final: 0.7416 (p0) REVERT: A 153 VAL cc_start: 0.8611 (t) cc_final: 0.8284 (p) REVERT: B 84 ASN cc_start: 0.7950 (t0) cc_final: 0.7733 (t0) REVERT: B 142 MET cc_start: 0.6995 (mmm) cc_final: 0.6580 (mmm) REVERT: B 174 ASP cc_start: 0.6921 (m-30) cc_final: 0.6221 (m-30) REVERT: B 177 TYR cc_start: 0.7426 (m-80) cc_final: 0.6579 (m-80) REVERT: B 186 ASN cc_start: 0.8199 (t0) cc_final: 0.7733 (t0) REVERT: B 188 GLU cc_start: 0.6954 (pm20) cc_final: 0.6157 (mp0) REVERT: B 212 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6670 (p0) REVERT: B 226 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7475 (tm-30) REVERT: C 8 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7324 (mttt) REVERT: C 14 ASP cc_start: 0.7210 (t0) cc_final: 0.6986 (t70) REVERT: C 54 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7234 (mtm-85) REVERT: C 124 MET cc_start: 0.7450 (ttp) cc_final: 0.7146 (tmm) REVERT: C 126 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6706 (mm-30) REVERT: C 127 ILE cc_start: 0.8591 (mm) cc_final: 0.8361 (tp) REVERT: C 130 MET cc_start: 0.7867 (tpp) cc_final: 0.7152 (tpp) REVERT: C 169 LYS cc_start: 0.7976 (tmtt) cc_final: 0.7566 (tmtt) REVERT: C 177 ILE cc_start: 0.7988 (mm) cc_final: 0.7622 (tp) REVERT: C 191 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8346 (mtmm) REVERT: C 197 ARG cc_start: 0.7164 (mtp-110) cc_final: 0.6688 (mtp85) REVERT: C 279 LYS cc_start: 0.8643 (ptmm) cc_final: 0.8432 (ptmm) REVERT: C 283 LYS cc_start: 0.7693 (tppt) cc_final: 0.7332 (tppt) REVERT: C 300 ASP cc_start: 0.6767 (m-30) cc_final: 0.6547 (m-30) REVERT: C 366 ILE cc_start: 0.8246 (mm) cc_final: 0.8013 (mm) REVERT: C 392 GLU cc_start: 0.7685 (tp30) cc_final: 0.7114 (tp30) REVERT: C 394 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7460 (ttm110) REVERT: C 403 MET cc_start: 0.7523 (ttm) cc_final: 0.7300 (ttm) REVERT: C 425 ILE cc_start: 0.8412 (tp) cc_final: 0.7803 (tt) REVERT: C 426 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8346 (pp) REVERT: C 427 ASP cc_start: 0.8149 (m-30) cc_final: 0.7857 (m-30) REVERT: C 429 MET cc_start: 0.8268 (mtt) cc_final: 0.7783 (mtm) REVERT: C 447 HIS cc_start: 0.7631 (t-170) cc_final: 0.7304 (t-170) REVERT: C 461 GLU cc_start: 0.7927 (tt0) cc_final: 0.6999 (tp30) REVERT: C 524 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7570 (tp) REVERT: C 540 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8212 (mtm110) REVERT: C 541 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 553 THR cc_start: 0.8201 (p) cc_final: 0.7988 (p) REVERT: C 620 ASN cc_start: 0.7982 (p0) cc_final: 0.7765 (p0) REVERT: C 668 ILE cc_start: 0.8260 (mm) cc_final: 0.8049 (mt) REVERT: C 674 ASP cc_start: 0.7923 (t0) cc_final: 0.7594 (t0) REVERT: C 688 GLN cc_start: 0.7826 (tt0) cc_final: 0.7602 (tt0) REVERT: C 719 LYS cc_start: 0.7430 (tptp) cc_final: 0.7122 (mmmt) REVERT: C 737 ASN cc_start: 0.8439 (m-40) cc_final: 0.7433 (m-40) REVERT: C 758 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.8160 (ttt90) REVERT: C 761 GLN cc_start: 0.7731 (mm110) cc_final: 0.7154 (mp10) REVERT: C 793 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6543 (mt-10) REVERT: C 800 MET cc_start: 0.7666 (ptp) cc_final: 0.7335 (ptm) REVERT: C 814 ASP cc_start: 0.7432 (t0) cc_final: 0.7187 (t0) REVERT: C 825 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7522 (mm-30) REVERT: C 853 ASP cc_start: 0.8245 (m-30) cc_final: 0.7663 (p0) REVERT: C 928 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8703 (m) REVERT: C 930 ASP cc_start: 0.7079 (t0) cc_final: 0.6869 (t0) REVERT: C 951 MET cc_start: 0.8561 (mtp) cc_final: 0.8027 (mtp) REVERT: C 954 LYS cc_start: 0.8583 (mtmm) cc_final: 0.7636 (mtmt) REVERT: C 955 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7673 (tp-100) REVERT: C 957 LYS cc_start: 0.9026 (pptt) cc_final: 0.8616 (pptt) REVERT: C 1030 GLU cc_start: 0.8474 (tp30) cc_final: 0.8215 (tp30) REVERT: C 1053 TYR cc_start: 0.8209 (m-80) cc_final: 0.7675 (m-80) REVERT: C 1119 MET cc_start: 0.7722 (tpp) cc_final: 0.7385 (tmm) REVERT: C 1127 LYS cc_start: 0.7898 (tppp) cc_final: 0.7606 (tppt) REVERT: C 1131 MET cc_start: 0.7705 (tpp) cc_final: 0.7394 (tpp) REVERT: C 1142 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7592 (mtt-85) REVERT: C 1178 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8184 (mmtt) REVERT: C 1180 MET cc_start: 0.7402 (tpt) cc_final: 0.7194 (tmm) REVERT: C 1191 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8097 (mmmt) REVERT: C 1200 LYS cc_start: 0.8258 (tptp) cc_final: 0.8024 (tptp) REVERT: C 1279 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7179 (mm-30) REVERT: C 1290 MET cc_start: 0.7519 (tmm) cc_final: 0.7169 (tmm) REVERT: C 1303 LYS cc_start: 0.8045 (tppp) cc_final: 0.7627 (ttmm) REVERT: C 1321 GLU cc_start: 0.6851 (pm20) cc_final: 0.6471 (pp20) REVERT: C 1329 GLU cc_start: 0.7482 (tt0) cc_final: 0.6523 (mt-10) REVERT: C 1338 GLU cc_start: 0.6960 (pp20) cc_final: 0.6344 (pp20) REVERT: D 21 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7469 (mmtt) REVERT: D 32 SER cc_start: 0.8795 (m) cc_final: 0.8570 (p) REVERT: D 35 PHE cc_start: 0.6853 (m-80) cc_final: 0.6440 (m-80) REVERT: D 50 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8650 (tmtt) REVERT: D 69 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7050 (tm-30) REVERT: D 84 ILE cc_start: 0.7757 (pt) cc_final: 0.7470 (mp) REVERT: D 94 GLN cc_start: 0.6929 (tp40) cc_final: 0.6721 (tp40) REVERT: D 115 TRP cc_start: 0.8648 (OUTLIER) cc_final: 0.8154 (m-10) REVERT: D 141 PHE cc_start: 0.7753 (m-10) cc_final: 0.7498 (m-10) REVERT: D 179 LYS cc_start: 0.8404 (mttt) cc_final: 0.7638 (tttt) REVERT: D 183 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7541 (tm-30) REVERT: D 190 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7386 (ptpp) REVERT: D 198 CYS cc_start: 0.8039 (m) cc_final: 0.7779 (m) REVERT: D 200 GLN cc_start: 0.8250 (pp30) cc_final: 0.7691 (pp30) REVERT: D 203 GLU cc_start: 0.8582 (pp20) cc_final: 0.8340 (pp20) REVERT: D 211 GLU cc_start: 0.8254 (pp20) cc_final: 0.7738 (pp20) REVERT: D 215 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8242 (mmtm) REVERT: D 219 LYS cc_start: 0.8481 (mttt) cc_final: 0.8137 (mttt) REVERT: D 222 LYS cc_start: 0.8337 (mptt) cc_final: 0.8002 (mptt) REVERT: D 225 GLU cc_start: 0.7982 (tp30) cc_final: 0.7782 (tp30) REVERT: D 233 LYS cc_start: 0.8282 (mmmm) cc_final: 0.7995 (mmmm) REVERT: D 237 MET cc_start: 0.7945 (tpp) cc_final: 0.7681 (tpp) REVERT: D 241 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7791 (p) REVERT: D 278 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7732 (ttm-80) REVERT: D 294 ASN cc_start: 0.8166 (t0) cc_final: 0.6706 (t0) REVERT: D 295 GLU cc_start: 0.7998 (tt0) cc_final: 0.7562 (tt0) REVERT: D 297 ARG cc_start: 0.8336 (tmm-80) cc_final: 0.7773 (tmm-80) REVERT: D 298 MET cc_start: 0.7726 (mmp) cc_final: 0.6656 (mmt) REVERT: D 301 GLU cc_start: 0.7883 (tp30) cc_final: 0.7471 (tm-30) REVERT: D 311 ARG cc_start: 0.7435 (tpp80) cc_final: 0.7182 (tpp80) REVERT: D 330 MET cc_start: 0.7590 (ttt) cc_final: 0.7109 (ttt) REVERT: D 341 ASN cc_start: 0.7971 (m-40) cc_final: 0.7371 (t0) REVERT: D 362 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7369 (mtm180) REVERT: D 378 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7942 (mtpp) REVERT: D 400 MET cc_start: 0.8303 (mtm) cc_final: 0.7252 (mtm) REVERT: D 405 GLU cc_start: 0.7070 (mp0) cc_final: 0.6674 (mp0) REVERT: D 417 ARG cc_start: 0.7545 (tpp80) cc_final: 0.7069 (ttp80) REVERT: D 431 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7757 (ttp-110) REVERT: D 432 LEU cc_start: 0.8407 (mm) cc_final: 0.8088 (mm) REVERT: D 479 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 506 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7962 (p) REVERT: D 511 TYR cc_start: 0.7738 (t80) cc_final: 0.7202 (t80) REVERT: D 531 LYS cc_start: 0.8348 (ttmt) cc_final: 0.8016 (ttmm) REVERT: D 556 GLU cc_start: 0.6716 (tp30) cc_final: 0.6008 (tm-30) REVERT: D 566 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7713 (mtpp) REVERT: D 587 LEU cc_start: 0.8311 (mm) cc_final: 0.8034 (mt) REVERT: D 604 MET cc_start: 0.7566 (tmm) cc_final: 0.7182 (tmm) REVERT: D 625 MET cc_start: 0.7915 (tmm) cc_final: 0.7618 (tmm) REVERT: D 629 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: D 644 MET cc_start: 0.8161 (mpp) cc_final: 0.7782 (mtm) REVERT: D 658 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8365 (mm-30) REVERT: D 678 ARG cc_start: 0.8604 (ppt170) cc_final: 0.8265 (ttp80) REVERT: D 697 MET cc_start: 0.7900 (tmm) cc_final: 0.7600 (tmm) REVERT: D 698 MET cc_start: 0.7741 (tpt) cc_final: 0.7366 (tpp) REVERT: D 703 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7655 (m) REVERT: D 715 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7820 (tppt) REVERT: D 722 ILE cc_start: 0.8442 (tp) cc_final: 0.8200 (tt) REVERT: D 724 MET cc_start: 0.7947 (ttp) cc_final: 0.7600 (mtp) REVERT: D 728 SER cc_start: 0.8420 (p) cc_final: 0.7850 (t) REVERT: D 738 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7310 (ttm110) REVERT: D 757 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8320 (m) REVERT: D 765 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6868 (tm-30) REVERT: D 781 LYS cc_start: 0.8735 (tptp) cc_final: 0.8280 (tppt) REVERT: D 789 LYS cc_start: 0.7973 (ptmm) cc_final: 0.7580 (tttt) REVERT: D 805 GLN cc_start: 0.7817 (pm20) cc_final: 0.7371 (pm20) REVERT: D 806 ASP cc_start: 0.7617 (p0) cc_final: 0.6650 (t0) REVERT: D 808 VAL cc_start: 0.8429 (t) cc_final: 0.8113 (p) REVERT: D 811 GLU cc_start: 0.7647 (tp30) cc_final: 0.7258 (tp30) REVERT: D 821 MET cc_start: 0.7514 (tpt) cc_final: 0.7098 (pmm) REVERT: D 822 MET cc_start: 0.7786 (tpp) cc_final: 0.7488 (tpt) REVERT: D 850 LYS cc_start: 0.8659 (tmtt) cc_final: 0.8312 (tptp) REVERT: D 873 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8015 (mt-10) REVERT: D 877 VAL cc_start: 0.8093 (t) cc_final: 0.7844 (p) REVERT: D 911 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8500 (ttmt) REVERT: D 981 GLU cc_start: 0.7596 (tp30) cc_final: 0.7210 (tp30) REVERT: D 983 LYS cc_start: 0.7362 (mptt) cc_final: 0.6995 (ptpt) REVERT: D 992 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7797 (mmtt) REVERT: D 1015 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7045 (pt0) REVERT: D 1095 MET cc_start: 0.6278 (pmm) cc_final: 0.6010 (pmm) REVERT: D 1119 ASP cc_start: 0.7772 (t0) cc_final: 0.7377 (m-30) REVERT: D 1144 LEU cc_start: 0.8718 (mm) cc_final: 0.8507 (mm) REVERT: D 1146 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8106 (mm-30) REVERT: D 1189 MET cc_start: 0.7196 (mmp) cc_final: 0.6821 (mmp) REVERT: D 1231 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.6537 (ttm-80) REVERT: D 1247 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7609 (ttmt) REVERT: D 1292 LEU cc_start: 0.8465 (tp) cc_final: 0.8205 (tp) REVERT: D 1334 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7485 (mm-30) REVERT: D 1342 ASP cc_start: 0.7065 (t0) cc_final: 0.6850 (t0) REVERT: D 1352 ILE cc_start: 0.8398 (tp) cc_final: 0.7911 (tt) REVERT: E 11 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: E 68 GLU cc_start: 0.8175 (tp30) cc_final: 0.7874 (tp30) outliers start: 88 outliers final: 53 residues processed: 811 average time/residue: 0.4772 time to fit residues: 572.9124 Evaluate side-chains 824 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 759 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 950 GLU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 152 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 760 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26848 Z= 0.210 Angle : 0.625 12.624 36556 Z= 0.320 Chirality : 0.043 0.189 4184 Planarity : 0.004 0.056 4544 Dihedral : 14.712 174.573 4287 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.55 % Allowed : 17.61 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.97 (0.14), residues: 3164 helix: 0.71 (0.16), residues: 1067 sheet: -0.32 (0.28), residues: 329 loop : -1.64 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 33 HIS 0.016 0.001 HIS B 132 PHE 0.024 0.001 PHE C 224 TYR 0.020 0.001 TYR C 70 ARG 0.008 0.001 ARG C1156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 774 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7880 (mtpp) REVERT: A 80 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6787 (tm-30) REVERT: A 118 ASP cc_start: 0.7888 (p0) cc_final: 0.7361 (p0) REVERT: A 120 ASP cc_start: 0.7921 (p0) cc_final: 0.7500 (p0) REVERT: A 153 VAL cc_start: 0.8594 (t) cc_final: 0.8312 (p) REVERT: B 33 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7457 (ttp80) REVERT: B 60 GLU cc_start: 0.6118 (tp30) cc_final: 0.5539 (tp30) REVERT: B 84 ASN cc_start: 0.7949 (t0) cc_final: 0.7745 (t0) REVERT: B 140 ILE cc_start: 0.8079 (tp) cc_final: 0.7287 (tp) REVERT: B 142 MET cc_start: 0.7010 (mmm) cc_final: 0.6252 (mmm) REVERT: B 174 ASP cc_start: 0.6953 (m-30) cc_final: 0.6251 (m-30) REVERT: B 186 ASN cc_start: 0.8197 (t0) cc_final: 0.7716 (t0) REVERT: B 188 GLU cc_start: 0.6878 (pm20) cc_final: 0.6063 (mp0) REVERT: B 212 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6529 (p0) REVERT: B 226 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 8 LYS cc_start: 0.7826 (mtpp) cc_final: 0.7289 (mttt) REVERT: C 14 ASP cc_start: 0.7230 (t0) cc_final: 0.6982 (t0) REVERT: C 54 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.7105 (mtm-85) REVERT: C 124 MET cc_start: 0.7457 (ttp) cc_final: 0.6441 (tmm) REVERT: C 169 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7537 (tmtt) REVERT: C 177 ILE cc_start: 0.7929 (mm) cc_final: 0.7603 (tp) REVERT: C 191 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8326 (mtmm) REVERT: C 197 ARG cc_start: 0.7161 (mtp-110) cc_final: 0.6696 (mtp85) REVERT: C 218 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7632 (tm-30) REVERT: C 219 GLN cc_start: 0.8470 (mt0) cc_final: 0.8224 (mt0) REVERT: C 342 ASP cc_start: 0.7622 (t0) cc_final: 0.7347 (t0) REVERT: C 358 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7503 (t70) REVERT: C 366 ILE cc_start: 0.8251 (mm) cc_final: 0.8032 (mm) REVERT: C 392 GLU cc_start: 0.7672 (tp30) cc_final: 0.7098 (tp30) REVERT: C 394 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7361 (ttm110) REVERT: C 427 ASP cc_start: 0.8121 (m-30) cc_final: 0.7792 (m-30) REVERT: C 447 HIS cc_start: 0.7654 (t-170) cc_final: 0.7241 (t-170) REVERT: C 461 GLU cc_start: 0.7989 (tt0) cc_final: 0.7025 (tp30) REVERT: C 524 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7477 (tp) REVERT: C 540 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.8191 (mtm110) REVERT: C 541 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 668 ILE cc_start: 0.8265 (mm) cc_final: 0.8045 (mt) REVERT: C 674 ASP cc_start: 0.7829 (t0) cc_final: 0.7411 (t0) REVERT: C 719 LYS cc_start: 0.7424 (tptp) cc_final: 0.7100 (mmmt) REVERT: C 737 ASN cc_start: 0.8457 (m-40) cc_final: 0.7475 (m-40) REVERT: C 761 GLN cc_start: 0.7628 (mm110) cc_final: 0.7226 (mp10) REVERT: C 793 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6751 (mt-10) REVERT: C 800 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7268 (ptm) REVERT: C 820 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: C 825 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7490 (mm-30) REVERT: C 853 ASP cc_start: 0.8251 (m-30) cc_final: 0.7685 (p0) REVERT: C 864 LYS cc_start: 0.7664 (mmtp) cc_final: 0.7322 (mmtp) REVERT: C 930 ASP cc_start: 0.7127 (t0) cc_final: 0.6856 (t0) REVERT: C 951 MET cc_start: 0.8544 (mtp) cc_final: 0.8174 (mtp) REVERT: C 954 LYS cc_start: 0.8550 (mtmm) cc_final: 0.7800 (mtmm) REVERT: C 955 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7663 (tp-100) REVERT: C 957 LYS cc_start: 0.9049 (pptt) cc_final: 0.8623 (pptt) REVERT: C 1030 GLU cc_start: 0.8471 (tp30) cc_final: 0.8129 (tp30) REVERT: C 1053 TYR cc_start: 0.8182 (m-80) cc_final: 0.7727 (m-80) REVERT: C 1079 ILE cc_start: 0.8393 (mm) cc_final: 0.7910 (mt) REVERT: C 1119 MET cc_start: 0.7710 (tpp) cc_final: 0.7412 (tmm) REVERT: C 1127 LYS cc_start: 0.7941 (tppp) cc_final: 0.7732 (tppt) REVERT: C 1131 MET cc_start: 0.7669 (tpp) cc_final: 0.7431 (tpp) REVERT: C 1142 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7680 (mtt-85) REVERT: C 1146 GLN cc_start: 0.8145 (tp40) cc_final: 0.7516 (tp40) REVERT: C 1178 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8243 (mmtt) REVERT: C 1191 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8093 (mmmt) REVERT: C 1192 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7533 (mp0) REVERT: C 1200 LYS cc_start: 0.8245 (tptp) cc_final: 0.8038 (tptp) REVERT: C 1220 GLN cc_start: 0.7172 (tp-100) cc_final: 0.6967 (tp-100) REVERT: C 1279 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7075 (mm-30) REVERT: C 1289 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7816 (tm-30) REVERT: C 1290 MET cc_start: 0.7747 (tmm) cc_final: 0.7503 (tmm) REVERT: C 1303 LYS cc_start: 0.8035 (tppp) cc_final: 0.7665 (ttmm) REVERT: C 1304 MET cc_start: 0.7229 (tpp) cc_final: 0.6930 (tpp) REVERT: C 1329 GLU cc_start: 0.7454 (tt0) cc_final: 0.6703 (mt-10) REVERT: C 1338 GLU cc_start: 0.6824 (pp20) cc_final: 0.6248 (pp20) REVERT: C 1340 GLU cc_start: 0.6557 (mp0) cc_final: 0.5990 (mp0) REVERT: D 21 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7127 (mmmm) REVERT: D 32 SER cc_start: 0.8794 (m) cc_final: 0.8587 (p) REVERT: D 35 PHE cc_start: 0.6814 (m-80) cc_final: 0.6415 (m-80) REVERT: D 50 LYS cc_start: 0.8906 (tmtt) cc_final: 0.8677 (tmtt) REVERT: D 69 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7091 (tm-30) REVERT: D 84 ILE cc_start: 0.7791 (pt) cc_final: 0.7495 (mp) REVERT: D 94 GLN cc_start: 0.7081 (tp40) cc_final: 0.6629 (tp40) REVERT: D 104 HIS cc_start: 0.7584 (p-80) cc_final: 0.7312 (p90) REVERT: D 115 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.8192 (m-10) REVERT: D 117 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7654 (mm) REVERT: D 141 PHE cc_start: 0.7778 (m-10) cc_final: 0.7466 (m-10) REVERT: D 179 LYS cc_start: 0.8362 (mttt) cc_final: 0.7716 (mmmm) REVERT: D 180 MET cc_start: 0.6849 (ppp) cc_final: 0.6438 (ppp) REVERT: D 183 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 190 LYS cc_start: 0.7918 (ptpp) cc_final: 0.7333 (ptpp) REVERT: D 200 GLN cc_start: 0.8228 (pp30) cc_final: 0.7674 (pp30) REVERT: D 203 GLU cc_start: 0.8551 (pp20) cc_final: 0.8307 (pp20) REVERT: D 211 GLU cc_start: 0.8165 (pp20) cc_final: 0.7609 (pp20) REVERT: D 215 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8195 (mmtm) REVERT: D 219 LYS cc_start: 0.8485 (mttt) cc_final: 0.8133 (mttt) REVERT: D 222 LYS cc_start: 0.8352 (mptt) cc_final: 0.7988 (mptt) REVERT: D 225 GLU cc_start: 0.7957 (tp30) cc_final: 0.7739 (tp30) REVERT: D 233 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7905 (mmmm) REVERT: D 236 TRP cc_start: 0.8812 (m-10) cc_final: 0.8435 (m-10) REVERT: D 241 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7752 (p) REVERT: D 278 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7733 (ttm-80) REVERT: D 294 ASN cc_start: 0.8170 (t0) cc_final: 0.6770 (t0) REVERT: D 295 GLU cc_start: 0.7936 (tt0) cc_final: 0.7547 (tt0) REVERT: D 297 ARG cc_start: 0.8316 (tmm-80) cc_final: 0.7726 (tmm-80) REVERT: D 298 MET cc_start: 0.7742 (mmp) cc_final: 0.6588 (mmt) REVERT: D 301 GLU cc_start: 0.7883 (tp30) cc_final: 0.7405 (tm-30) REVERT: D 330 MET cc_start: 0.7559 (ttt) cc_final: 0.7094 (ttt) REVERT: D 335 GLN cc_start: 0.7826 (mp-120) cc_final: 0.7614 (mp10) REVERT: D 370 LYS cc_start: 0.7751 (tttt) cc_final: 0.7474 (tttp) REVERT: D 378 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7945 (mmmm) REVERT: D 398 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8103 (mmmt) REVERT: D 400 MET cc_start: 0.8293 (mtm) cc_final: 0.7688 (mtm) REVERT: D 417 ARG cc_start: 0.7507 (tpp80) cc_final: 0.6787 (ttp80) REVERT: D 418 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7034 (mm-30) REVERT: D 431 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7752 (ttp-110) REVERT: D 432 LEU cc_start: 0.8400 (mm) cc_final: 0.8034 (mm) REVERT: D 466 MET cc_start: 0.7751 (mmp) cc_final: 0.7519 (mmp) REVERT: D 479 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 506 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7920 (p) REVERT: D 511 TYR cc_start: 0.7701 (t80) cc_final: 0.7167 (t80) REVERT: D 531 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7993 (ttmm) REVERT: D 556 GLU cc_start: 0.6627 (tp30) cc_final: 0.5951 (tm-30) REVERT: D 566 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7727 (mtpp) REVERT: D 604 MET cc_start: 0.7522 (tmm) cc_final: 0.7165 (tmm) REVERT: D 644 MET cc_start: 0.8122 (mpp) cc_final: 0.7597 (mtm) REVERT: D 678 ARG cc_start: 0.8607 (ppt170) cc_final: 0.8260 (ttp80) REVERT: D 692 ARG cc_start: 0.8259 (ttm110) cc_final: 0.7960 (ttm110) REVERT: D 697 MET cc_start: 0.7864 (tmm) cc_final: 0.7571 (tmm) REVERT: D 698 MET cc_start: 0.7740 (tpt) cc_final: 0.7351 (tpp) REVERT: D 703 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7643 (m) REVERT: D 715 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7784 (tppt) REVERT: D 722 ILE cc_start: 0.8392 (tp) cc_final: 0.8172 (tt) REVERT: D 724 MET cc_start: 0.7914 (ttp) cc_final: 0.7634 (mtp) REVERT: D 728 SER cc_start: 0.8333 (p) cc_final: 0.7837 (t) REVERT: D 738 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7414 (ttm110) REVERT: D 757 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 765 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6874 (tm-30) REVERT: D 781 LYS cc_start: 0.8736 (tptp) cc_final: 0.8295 (tppt) REVERT: D 806 ASP cc_start: 0.7564 (p0) cc_final: 0.6633 (t0) REVERT: D 808 VAL cc_start: 0.8502 (t) cc_final: 0.8161 (p) REVERT: D 811 GLU cc_start: 0.7701 (tp30) cc_final: 0.7192 (tp30) REVERT: D 821 MET cc_start: 0.7533 (tpt) cc_final: 0.7185 (pmm) REVERT: D 850 LYS cc_start: 0.8648 (tmtt) cc_final: 0.8385 (tptt) REVERT: D 873 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 877 VAL cc_start: 0.8193 (t) cc_final: 0.7951 (p) REVERT: D 983 LYS cc_start: 0.7454 (mptt) cc_final: 0.7108 (ptpt) REVERT: D 992 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7752 (mmtt) REVERT: D 1007 ASP cc_start: 0.8113 (t70) cc_final: 0.7853 (t0) REVERT: D 1040 MET cc_start: 0.6822 (tpp) cc_final: 0.4472 (mmt) REVERT: D 1095 MET cc_start: 0.6221 (pmm) cc_final: 0.5949 (pmm) REVERT: D 1101 LEU cc_start: 0.8508 (tp) cc_final: 0.7573 (pp) REVERT: D 1119 ASP cc_start: 0.7803 (t0) cc_final: 0.7454 (m-30) REVERT: D 1146 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8122 (mm-30) REVERT: D 1189 MET cc_start: 0.7178 (mmp) cc_final: 0.6812 (mmp) REVERT: D 1222 ARG cc_start: 0.8560 (ptm-80) cc_final: 0.7955 (ptm-80) REVERT: D 1223 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7757 (mm) REVERT: D 1231 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.6555 (ttm-80) REVERT: D 1247 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7652 (ttmt) REVERT: D 1292 LEU cc_start: 0.8464 (tp) cc_final: 0.8232 (tp) REVERT: D 1327 GLU cc_start: 0.7747 (tp30) cc_final: 0.7119 (tm-30) REVERT: D 1334 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7441 (mm-30) REVERT: D 1352 ILE cc_start: 0.8321 (tp) cc_final: 0.7944 (tt) REVERT: E 11 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: E 59 ILE cc_start: 0.8058 (mp) cc_final: 0.7622 (mp) REVERT: E 68 GLU cc_start: 0.8182 (tp30) cc_final: 0.7855 (tp30) outliers start: 96 outliers final: 64 residues processed: 808 average time/residue: 0.4486 time to fit residues: 534.8579 Evaluate side-chains 839 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 761 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 265 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 0.3980 chunk 279 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 760 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26848 Z= 0.192 Angle : 0.622 12.500 36556 Z= 0.316 Chirality : 0.042 0.236 4184 Planarity : 0.004 0.055 4544 Dihedral : 14.658 174.171 4287 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.14 % Allowed : 18.91 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.92 (0.14), residues: 3164 helix: 0.73 (0.16), residues: 1068 sheet: -0.27 (0.28), residues: 326 loop : -1.59 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 33 HIS 0.007 0.001 HIS C1023 PHE 0.015 0.001 PHE C 514 TYR 0.026 0.001 TYR C 70 ARG 0.008 0.000 ARG D1369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 772 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7881 (mtpp) REVERT: A 80 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 102 LEU cc_start: 0.8296 (tp) cc_final: 0.7983 (tp) REVERT: A 118 ASP cc_start: 0.7883 (p0) cc_final: 0.7372 (p0) REVERT: A 120 ASP cc_start: 0.7887 (p0) cc_final: 0.7368 (p0) REVERT: A 153 VAL cc_start: 0.8584 (t) cc_final: 0.8289 (p) REVERT: A 211 ILE cc_start: 0.8269 (pt) cc_final: 0.8023 (mt) REVERT: B 33 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7399 (ttp80) REVERT: B 60 GLU cc_start: 0.6214 (tp30) cc_final: 0.5665 (tp30) REVERT: B 140 ILE cc_start: 0.7976 (tp) cc_final: 0.7091 (tp) REVERT: B 142 MET cc_start: 0.7004 (mmm) cc_final: 0.6278 (mmm) REVERT: B 174 ASP cc_start: 0.6954 (m-30) cc_final: 0.6228 (m-30) REVERT: B 186 ASN cc_start: 0.8167 (t0) cc_final: 0.7790 (t0) REVERT: B 188 GLU cc_start: 0.6711 (pm20) cc_final: 0.6072 (mp0) REVERT: B 212 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6426 (p0) REVERT: B 226 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7491 (tm-30) REVERT: C 8 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7280 (mttt) REVERT: C 22 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8221 (mt) REVERT: C 46 GLN cc_start: 0.6830 (pm20) cc_final: 0.6605 (pm20) REVERT: C 54 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7103 (mtm-85) REVERT: C 124 MET cc_start: 0.7468 (ttp) cc_final: 0.6399 (tmm) REVERT: C 169 LYS cc_start: 0.7977 (tmtt) cc_final: 0.7523 (tmtt) REVERT: C 177 ILE cc_start: 0.7921 (mm) cc_final: 0.7586 (tp) REVERT: C 191 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8264 (mtmm) REVERT: C 197 ARG cc_start: 0.7147 (mtp-110) cc_final: 0.6671 (mtp85) REVERT: C 218 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 219 GLN cc_start: 0.8458 (mt0) cc_final: 0.8198 (mt0) REVERT: C 278 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8162 (pp20) REVERT: C 299 LYS cc_start: 0.8064 (ptmt) cc_final: 0.7707 (ptmm) REVERT: C 342 ASP cc_start: 0.7700 (t0) cc_final: 0.7419 (t0) REVERT: C 358 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7179 (t0) REVERT: C 392 GLU cc_start: 0.7700 (tp30) cc_final: 0.7169 (tp30) REVERT: C 403 MET cc_start: 0.7392 (ttm) cc_final: 0.7168 (ttm) REVERT: C 427 ASP cc_start: 0.8107 (m-30) cc_final: 0.7806 (m-30) REVERT: C 447 HIS cc_start: 0.7642 (t-170) cc_final: 0.7199 (t-170) REVERT: C 461 GLU cc_start: 0.7977 (tt0) cc_final: 0.7142 (tm-30) REVERT: C 504 GLU cc_start: 0.7527 (pp20) cc_final: 0.7065 (pp20) REVERT: C 515 MET cc_start: 0.6314 (ttt) cc_final: 0.5722 (ttt) REVERT: C 540 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8135 (mtm110) REVERT: C 541 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7831 (mm-30) REVERT: C 623 LEU cc_start: 0.7959 (pp) cc_final: 0.7624 (pp) REVERT: C 668 ILE cc_start: 0.8254 (mm) cc_final: 0.8042 (mt) REVERT: C 674 ASP cc_start: 0.7831 (t0) cc_final: 0.7346 (t0) REVERT: C 719 LYS cc_start: 0.7404 (tptp) cc_final: 0.7080 (mmmt) REVERT: C 737 ASN cc_start: 0.8448 (m-40) cc_final: 0.7574 (m110) REVERT: C 760 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8001 (t0) REVERT: C 761 GLN cc_start: 0.7525 (mm110) cc_final: 0.6904 (mp10) REVERT: C 779 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.7678 (ttm-80) REVERT: C 800 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7263 (ptm) REVERT: C 820 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: C 825 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7482 (mm-30) REVERT: C 853 ASP cc_start: 0.8246 (m-30) cc_final: 0.7611 (p0) REVERT: C 864 LYS cc_start: 0.7670 (mmtp) cc_final: 0.7341 (mmtp) REVERT: C 928 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8646 (m) REVERT: C 930 ASP cc_start: 0.7097 (t0) cc_final: 0.6852 (t0) REVERT: C 951 MET cc_start: 0.8562 (mtp) cc_final: 0.8128 (mtp) REVERT: C 954 LYS cc_start: 0.8519 (mtmm) cc_final: 0.7761 (mtmm) REVERT: C 955 GLN cc_start: 0.8322 (tp-100) cc_final: 0.7674 (tp-100) REVERT: C 957 LYS cc_start: 0.9038 (pptt) cc_final: 0.8592 (pptt) REVERT: C 1030 GLU cc_start: 0.8528 (tp30) cc_final: 0.8104 (tp30) REVERT: C 1079 ILE cc_start: 0.8334 (mm) cc_final: 0.7594 (mt) REVERT: C 1107 MET cc_start: 0.6918 (ptm) cc_final: 0.6615 (ptm) REVERT: C 1119 MET cc_start: 0.7716 (tpp) cc_final: 0.7405 (tmm) REVERT: C 1131 MET cc_start: 0.7635 (tpp) cc_final: 0.7412 (tpp) REVERT: C 1142 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7397 (mtt-85) REVERT: C 1146 GLN cc_start: 0.8134 (tp40) cc_final: 0.7524 (tp40) REVERT: C 1164 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: C 1178 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8240 (mmtt) REVERT: C 1191 LYS cc_start: 0.8381 (mmmt) cc_final: 0.8161 (mmmt) REVERT: C 1192 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7540 (mp0) REVERT: C 1200 LYS cc_start: 0.8236 (tptp) cc_final: 0.8030 (tptp) REVERT: C 1279 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7053 (mm-30) REVERT: C 1289 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 1290 MET cc_start: 0.7796 (tmm) cc_final: 0.7562 (tmm) REVERT: C 1303 LYS cc_start: 0.8059 (tppp) cc_final: 0.7704 (ttmm) REVERT: C 1329 GLU cc_start: 0.7427 (tt0) cc_final: 0.6964 (mt-10) REVERT: C 1338 GLU cc_start: 0.6760 (pp20) cc_final: 0.6232 (pp20) REVERT: C 1340 GLU cc_start: 0.6689 (mp0) cc_final: 0.6326 (mp0) REVERT: D 35 PHE cc_start: 0.6733 (m-80) cc_final: 0.6359 (m-80) REVERT: D 50 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8485 (tptp) REVERT: D 66 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7943 (mmmm) REVERT: D 69 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7042 (tm-30) REVERT: D 84 ILE cc_start: 0.7806 (pt) cc_final: 0.7550 (mp) REVERT: D 94 GLN cc_start: 0.7059 (tp40) cc_final: 0.6579 (tp40) REVERT: D 104 HIS cc_start: 0.7633 (p-80) cc_final: 0.7362 (p90) REVERT: D 115 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.8186 (m-10) REVERT: D 117 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7703 (mm) REVERT: D 130 MET cc_start: 0.7654 (mmt) cc_final: 0.7365 (mmm) REVERT: D 141 PHE cc_start: 0.7835 (m-10) cc_final: 0.7456 (m-10) REVERT: D 179 LYS cc_start: 0.8394 (mttt) cc_final: 0.7942 (mmmm) REVERT: D 180 MET cc_start: 0.6741 (ppp) cc_final: 0.6386 (ppp) REVERT: D 183 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7913 (tm-30) REVERT: D 190 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7361 (ptpp) REVERT: D 200 GLN cc_start: 0.8259 (pp30) cc_final: 0.7601 (pp30) REVERT: D 203 GLU cc_start: 0.8571 (pp20) cc_final: 0.8268 (pp20) REVERT: D 211 GLU cc_start: 0.8200 (pp20) cc_final: 0.7664 (pp20) REVERT: D 215 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8240 (mmtt) REVERT: D 219 LYS cc_start: 0.8460 (mttt) cc_final: 0.8041 (mttt) REVERT: D 222 LYS cc_start: 0.8376 (mptt) cc_final: 0.7981 (mptt) REVERT: D 225 GLU cc_start: 0.7966 (tp30) cc_final: 0.7744 (tp30) REVERT: D 233 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7788 (mmtm) REVERT: D 236 TRP cc_start: 0.8813 (m-10) cc_final: 0.8522 (m-10) REVERT: D 241 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7742 (p) REVERT: D 278 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7729 (ttm-80) REVERT: D 294 ASN cc_start: 0.8168 (t0) cc_final: 0.6762 (t0) REVERT: D 295 GLU cc_start: 0.7974 (tt0) cc_final: 0.7567 (tt0) REVERT: D 297 ARG cc_start: 0.8363 (tmm-80) cc_final: 0.7745 (tmm-80) REVERT: D 298 MET cc_start: 0.7833 (mmp) cc_final: 0.6699 (mmt) REVERT: D 301 GLU cc_start: 0.7890 (tp30) cc_final: 0.7410 (tm-30) REVERT: D 330 MET cc_start: 0.7522 (ttt) cc_final: 0.7257 (ttt) REVERT: D 378 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7882 (mmmm) REVERT: D 398 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8169 (mmmt) REVERT: D 400 MET cc_start: 0.8517 (mtm) cc_final: 0.7690 (mtm) REVERT: D 404 GLU cc_start: 0.7975 (pm20) cc_final: 0.7666 (pp20) REVERT: D 431 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7739 (ttp-110) REVERT: D 432 LEU cc_start: 0.8385 (mm) cc_final: 0.7978 (mm) REVERT: D 479 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7407 (tm-30) REVERT: D 506 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7973 (p) REVERT: D 511 TYR cc_start: 0.7639 (t80) cc_final: 0.7059 (t80) REVERT: D 513 MET cc_start: 0.7780 (tpt) cc_final: 0.7472 (tpp) REVERT: D 531 LYS cc_start: 0.8362 (ttmt) cc_final: 0.7979 (ttmm) REVERT: D 556 GLU cc_start: 0.6591 (tp30) cc_final: 0.5925 (tm-30) REVERT: D 566 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7728 (mtpp) REVERT: D 604 MET cc_start: 0.7499 (tmm) cc_final: 0.7165 (tmm) REVERT: D 625 MET cc_start: 0.7907 (tmm) cc_final: 0.7610 (tmm) REVERT: D 644 MET cc_start: 0.8076 (mpp) cc_final: 0.7624 (mtm) REVERT: D 678 ARG cc_start: 0.8611 (ppt170) cc_final: 0.8264 (ttp80) REVERT: D 697 MET cc_start: 0.7849 (tmm) cc_final: 0.7513 (tmm) REVERT: D 698 MET cc_start: 0.7730 (tpt) cc_final: 0.7352 (tpp) REVERT: D 702 GLN cc_start: 0.7972 (pt0) cc_final: 0.7574 (pp30) REVERT: D 703 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7208 (m) REVERT: D 715 LYS cc_start: 0.8352 (ttmm) cc_final: 0.7768 (tppt) REVERT: D 724 MET cc_start: 0.7930 (ttp) cc_final: 0.7643 (mtp) REVERT: D 728 SER cc_start: 0.8235 (p) cc_final: 0.7783 (t) REVERT: D 738 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7471 (ttm110) REVERT: D 765 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6706 (tm-30) REVERT: D 781 LYS cc_start: 0.8709 (tptp) cc_final: 0.8266 (tppt) REVERT: D 805 GLN cc_start: 0.7881 (pm20) cc_final: 0.7476 (pm20) REVERT: D 806 ASP cc_start: 0.7571 (p0) cc_final: 0.6646 (t0) REVERT: D 808 VAL cc_start: 0.8494 (t) cc_final: 0.8165 (p) REVERT: D 821 MET cc_start: 0.7553 (tpt) cc_final: 0.7266 (pmm) REVERT: D 850 LYS cc_start: 0.8673 (tmtt) cc_final: 0.8427 (tptt) REVERT: D 867 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7475 (tm-30) REVERT: D 873 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 877 VAL cc_start: 0.8220 (t) cc_final: 0.7959 (p) REVERT: D 983 LYS cc_start: 0.7495 (mptt) cc_final: 0.7179 (ptpp) REVERT: D 992 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7760 (mmtt) REVERT: D 1040 MET cc_start: 0.6690 (tpp) cc_final: 0.4486 (mmt) REVERT: D 1095 MET cc_start: 0.6201 (pmm) cc_final: 0.5990 (pmm) REVERT: D 1101 LEU cc_start: 0.8545 (tp) cc_final: 0.7610 (pp) REVERT: D 1119 ASP cc_start: 0.7892 (t0) cc_final: 0.7442 (m-30) REVERT: D 1146 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8102 (mm-30) REVERT: D 1189 MET cc_start: 0.7174 (mmp) cc_final: 0.6771 (mmp) REVERT: D 1222 ARG cc_start: 0.8556 (ptm-80) cc_final: 0.8155 (ptm-80) REVERT: D 1223 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7832 (mm) REVERT: D 1231 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.6613 (ttm-80) REVERT: D 1232 TYR cc_start: 0.8130 (t80) cc_final: 0.7845 (t80) REVERT: D 1247 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7638 (ttmt) REVERT: D 1292 LEU cc_start: 0.8471 (tp) cc_final: 0.8250 (tp) REVERT: D 1327 GLU cc_start: 0.7719 (tp30) cc_final: 0.7043 (tm-30) REVERT: D 1334 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7405 (mm-30) REVERT: D 1352 ILE cc_start: 0.8350 (tp) cc_final: 0.7940 (tt) REVERT: E 11 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: E 53 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6881 (mm-30) REVERT: E 59 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7359 (mp) REVERT: E 68 GLU cc_start: 0.8178 (tp30) cc_final: 0.7867 (tp30) outliers start: 112 outliers final: 69 residues processed: 820 average time/residue: 0.4518 time to fit residues: 550.9724 Evaluate side-chains 834 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 748 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1286 LYS Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 76 optimal weight: 0.0970 chunk 311 optimal weight: 0.9990 chunk 258 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** B 84 ASN B 132 HIS ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26848 Z= 0.182 Angle : 0.629 12.495 36556 Z= 0.318 Chirality : 0.042 0.285 4184 Planarity : 0.004 0.056 4544 Dihedral : 14.612 173.990 4287 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.69 % Allowed : 21.38 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.88 (0.15), residues: 3164 helix: 0.73 (0.16), residues: 1072 sheet: -0.22 (0.28), residues: 336 loop : -1.55 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 33 HIS 0.009 0.001 HIS C1023 PHE 0.016 0.001 PHE C 514 TYR 0.025 0.001 TYR D 995 ARG 0.009 0.000 ARG D1369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 774 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7849 (mtpp) REVERT: A 68 TYR cc_start: 0.8539 (m-10) cc_final: 0.8110 (m-10) REVERT: A 80 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6844 (tm-30) REVERT: A 102 LEU cc_start: 0.8324 (tp) cc_final: 0.7946 (tp) REVERT: A 118 ASP cc_start: 0.7869 (p0) cc_final: 0.7370 (p0) REVERT: A 120 ASP cc_start: 0.7831 (p0) cc_final: 0.7289 (p0) REVERT: A 153 VAL cc_start: 0.8511 (t) cc_final: 0.8232 (p) REVERT: A 211 ILE cc_start: 0.8244 (pt) cc_final: 0.8022 (mt) REVERT: B 33 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7514 (ttp80) REVERT: B 60 GLU cc_start: 0.6277 (tp30) cc_final: 0.5749 (tp30) REVERT: B 140 ILE cc_start: 0.7912 (tp) cc_final: 0.7067 (tp) REVERT: B 142 MET cc_start: 0.7036 (mmm) cc_final: 0.6336 (mmm) REVERT: B 186 ASN cc_start: 0.8185 (t0) cc_final: 0.7657 (t0) REVERT: B 188 GLU cc_start: 0.6717 (pm20) cc_final: 0.6059 (mp0) REVERT: B 212 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6372 (p0) REVERT: B 226 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 8 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7279 (mttt) REVERT: C 22 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8183 (mt) REVERT: C 54 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7195 (mtm-85) REVERT: C 124 MET cc_start: 0.7462 (ttp) cc_final: 0.6378 (tmm) REVERT: C 169 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7699 (tmtt) REVERT: C 177 ILE cc_start: 0.7846 (mm) cc_final: 0.7545 (tp) REVERT: C 191 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8306 (mtmm) REVERT: C 197 ARG cc_start: 0.7195 (mtp-110) cc_final: 0.6716 (mtp85) REVERT: C 215 TYR cc_start: 0.7694 (m-80) cc_final: 0.7453 (m-80) REVERT: C 217 THR cc_start: 0.7188 (m) cc_final: 0.6249 (t) REVERT: C 218 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7694 (tm-30) REVERT: C 219 GLN cc_start: 0.8435 (mt0) cc_final: 0.8178 (mt0) REVERT: C 278 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8176 (pp20) REVERT: C 299 LYS cc_start: 0.8062 (ptmt) cc_final: 0.7694 (ptmm) REVERT: C 342 ASP cc_start: 0.7684 (t0) cc_final: 0.7407 (t0) REVERT: C 392 GLU cc_start: 0.7691 (tp30) cc_final: 0.7142 (tp30) REVERT: C 394 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7282 (ttm110) REVERT: C 427 ASP cc_start: 0.8100 (m-30) cc_final: 0.7801 (m-30) REVERT: C 447 HIS cc_start: 0.7678 (t-170) cc_final: 0.7214 (t-170) REVERT: C 461 GLU cc_start: 0.7951 (tt0) cc_final: 0.7126 (tm-30) REVERT: C 504 GLU cc_start: 0.7519 (pp20) cc_final: 0.7111 (pp20) REVERT: C 541 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7842 (mm-30) REVERT: C 554 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7651 (m90) REVERT: C 623 LEU cc_start: 0.7925 (pp) cc_final: 0.7592 (pp) REVERT: C 668 ILE cc_start: 0.8269 (mm) cc_final: 0.8059 (mt) REVERT: C 674 ASP cc_start: 0.7810 (t0) cc_final: 0.7339 (t0) REVERT: C 719 LYS cc_start: 0.7392 (tptp) cc_final: 0.7162 (mmmt) REVERT: C 737 ASN cc_start: 0.8472 (m-40) cc_final: 0.7562 (m110) REVERT: C 779 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7798 (ttm-80) REVERT: C 800 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7242 (ptm) REVERT: C 820 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: C 825 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7478 (mm-30) REVERT: C 836 LEU cc_start: 0.7542 (mm) cc_final: 0.7048 (mp) REVERT: C 853 ASP cc_start: 0.8197 (m-30) cc_final: 0.7721 (p0) REVERT: C 864 LYS cc_start: 0.7671 (mmtp) cc_final: 0.7316 (mmtp) REVERT: C 928 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8652 (m) REVERT: C 943 LYS cc_start: 0.8696 (mmpt) cc_final: 0.8449 (mmtm) REVERT: C 951 MET cc_start: 0.8526 (mtp) cc_final: 0.8258 (mtp) REVERT: C 955 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7683 (tp-100) REVERT: C 957 LYS cc_start: 0.9027 (pptt) cc_final: 0.8576 (pptt) REVERT: C 1030 GLU cc_start: 0.8442 (tp30) cc_final: 0.8233 (tp30) REVERT: C 1079 ILE cc_start: 0.8345 (mm) cc_final: 0.7391 (mt) REVERT: C 1083 GLU cc_start: 0.7896 (pt0) cc_final: 0.7360 (pm20) REVERT: C 1107 MET cc_start: 0.6915 (ptm) cc_final: 0.6688 (ptm) REVERT: C 1119 MET cc_start: 0.7670 (tpp) cc_final: 0.7394 (tmm) REVERT: C 1146 GLN cc_start: 0.8156 (tp40) cc_final: 0.7565 (tp40) REVERT: C 1178 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8227 (mmtt) REVERT: C 1191 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8160 (mmmt) REVERT: C 1192 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7509 (mp0) REVERT: C 1200 LYS cc_start: 0.8223 (tptp) cc_final: 0.8016 (tptp) REVERT: C 1279 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7044 (mm-30) REVERT: C 1289 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 1290 MET cc_start: 0.7839 (tmm) cc_final: 0.7608 (tmm) REVERT: C 1303 LYS cc_start: 0.8083 (tppp) cc_final: 0.7722 (ttmm) REVERT: C 1315 MET cc_start: 0.6032 (mmp) cc_final: 0.5600 (tpp) REVERT: C 1329 GLU cc_start: 0.7395 (tt0) cc_final: 0.6876 (mt-10) REVERT: C 1332 SER cc_start: 0.8056 (p) cc_final: 0.7835 (p) REVERT: C 1340 GLU cc_start: 0.6782 (mp0) cc_final: 0.6481 (mp0) REVERT: D 35 PHE cc_start: 0.6619 (m-80) cc_final: 0.6322 (m-80) REVERT: D 50 LYS cc_start: 0.8894 (tmtt) cc_final: 0.8484 (tptp) REVERT: D 69 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7036 (tm-30) REVERT: D 84 ILE cc_start: 0.7827 (pt) cc_final: 0.7594 (mp) REVERT: D 94 GLN cc_start: 0.7056 (tp40) cc_final: 0.6791 (tp40) REVERT: D 104 HIS cc_start: 0.7636 (p-80) cc_final: 0.7317 (p90) REVERT: D 115 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: D 117 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7654 (mm) REVERT: D 124 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8156 (tt) REVERT: D 130 MET cc_start: 0.7637 (mmt) cc_final: 0.7324 (mmm) REVERT: D 141 PHE cc_start: 0.7846 (m-10) cc_final: 0.7441 (m-10) REVERT: D 179 LYS cc_start: 0.8382 (mttt) cc_final: 0.7936 (mmmm) REVERT: D 180 MET cc_start: 0.6733 (ppp) cc_final: 0.6364 (ppp) REVERT: D 183 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7910 (tm-30) REVERT: D 190 LYS cc_start: 0.7922 (ptpp) cc_final: 0.7345 (ptpp) REVERT: D 200 GLN cc_start: 0.8196 (pp30) cc_final: 0.7669 (pp30) REVERT: D 202 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8284 (mtm-85) REVERT: D 203 GLU cc_start: 0.8582 (pp20) cc_final: 0.8273 (pp20) REVERT: D 211 GLU cc_start: 0.8159 (pp20) cc_final: 0.7631 (pp20) REVERT: D 215 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8238 (mmtt) REVERT: D 219 LYS cc_start: 0.8463 (mttt) cc_final: 0.8036 (mttt) REVERT: D 222 LYS cc_start: 0.8391 (mptt) cc_final: 0.7956 (mptt) REVERT: D 233 LYS cc_start: 0.8229 (mmmm) cc_final: 0.7809 (mmtm) REVERT: D 236 TRP cc_start: 0.8828 (m-10) cc_final: 0.8564 (m-10) REVERT: D 241 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7733 (p) REVERT: D 294 ASN cc_start: 0.8161 (t0) cc_final: 0.6765 (t0) REVERT: D 295 GLU cc_start: 0.7877 (tt0) cc_final: 0.7466 (tt0) REVERT: D 297 ARG cc_start: 0.8344 (tmm-80) cc_final: 0.7733 (tmm-80) REVERT: D 298 MET cc_start: 0.7839 (mmp) cc_final: 0.6705 (mmt) REVERT: D 301 GLU cc_start: 0.7893 (tp30) cc_final: 0.7419 (tm-30) REVERT: D 339 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7202 (ttp-170) REVERT: D 370 LYS cc_start: 0.7818 (tttt) cc_final: 0.7563 (tttp) REVERT: D 378 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7737 (mmmm) REVERT: D 398 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8218 (mmmt) REVERT: D 400 MET cc_start: 0.8530 (mtm) cc_final: 0.7986 (mtt) REVERT: D 404 GLU cc_start: 0.7988 (pm20) cc_final: 0.7685 (pp20) REVERT: D 431 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.7711 (ttp-110) REVERT: D 432 LEU cc_start: 0.8383 (mm) cc_final: 0.7975 (mm) REVERT: D 443 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6965 (mm-30) REVERT: D 479 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 506 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7966 (p) REVERT: D 511 TYR cc_start: 0.7616 (t80) cc_final: 0.7043 (t80) REVERT: D 531 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7895 (ttmm) REVERT: D 556 GLU cc_start: 0.6533 (tp30) cc_final: 0.5883 (tm-30) REVERT: D 566 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7737 (mtpp) REVERT: D 604 MET cc_start: 0.7478 (tmm) cc_final: 0.7131 (tmm) REVERT: D 644 MET cc_start: 0.8080 (mpp) cc_final: 0.7619 (mtm) REVERT: D 678 ARG cc_start: 0.8627 (ppt170) cc_final: 0.7989 (ttp80) REVERT: D 681 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7851 (ttpp) REVERT: D 692 ARG cc_start: 0.8264 (ttm110) cc_final: 0.7859 (ttm110) REVERT: D 697 MET cc_start: 0.7853 (tmm) cc_final: 0.7531 (tmm) REVERT: D 698 MET cc_start: 0.7717 (tpt) cc_final: 0.7346 (tpp) REVERT: D 702 GLN cc_start: 0.7970 (pt0) cc_final: 0.7582 (pp30) REVERT: D 703 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7248 (m) REVERT: D 715 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7784 (tppt) REVERT: D 724 MET cc_start: 0.7931 (ttp) cc_final: 0.7659 (mtp) REVERT: D 728 SER cc_start: 0.8189 (p) cc_final: 0.7747 (t) REVERT: D 757 THR cc_start: 0.8477 (t) cc_final: 0.8245 (m) REVERT: D 765 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6805 (tm-30) REVERT: D 781 LYS cc_start: 0.8702 (tptp) cc_final: 0.8267 (tppt) REVERT: D 805 GLN cc_start: 0.7852 (pm20) cc_final: 0.7512 (pm20) REVERT: D 806 ASP cc_start: 0.7544 (p0) cc_final: 0.6635 (t0) REVERT: D 808 VAL cc_start: 0.8495 (t) cc_final: 0.8156 (p) REVERT: D 811 GLU cc_start: 0.7721 (tp30) cc_final: 0.7450 (tp30) REVERT: D 821 MET cc_start: 0.7475 (tpt) cc_final: 0.7018 (pmm) REVERT: D 850 LYS cc_start: 0.8626 (tmtt) cc_final: 0.8396 (tptt) REVERT: D 867 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7451 (tm-30) REVERT: D 873 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 877 VAL cc_start: 0.8238 (t) cc_final: 0.7974 (p) REVERT: D 964 LYS cc_start: 0.7974 (tppt) cc_final: 0.7719 (tppt) REVERT: D 983 LYS cc_start: 0.7583 (mptt) cc_final: 0.7375 (ptpp) REVERT: D 992 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7709 (mmtt) REVERT: D 993 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6182 (mm-30) REVERT: D 1007 ASP cc_start: 0.8137 (t70) cc_final: 0.7897 (t0) REVERT: D 1040 MET cc_start: 0.6654 (tpp) cc_final: 0.4435 (mmt) REVERT: D 1101 LEU cc_start: 0.8559 (tp) cc_final: 0.7626 (pp) REVERT: D 1119 ASP cc_start: 0.7898 (t0) cc_final: 0.7467 (m-30) REVERT: D 1146 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8102 (mm-30) REVERT: D 1189 MET cc_start: 0.7165 (mmp) cc_final: 0.6745 (mmp) REVERT: D 1232 TYR cc_start: 0.8120 (t80) cc_final: 0.7831 (t80) REVERT: D 1247 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7609 (ttmt) REVERT: D 1327 GLU cc_start: 0.7736 (tp30) cc_final: 0.7385 (tm-30) REVERT: D 1334 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7419 (mm-30) REVERT: D 1352 ILE cc_start: 0.8321 (tp) cc_final: 0.7931 (tt) REVERT: E 11 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: E 53 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6954 (mm-30) REVERT: E 59 ILE cc_start: 0.8013 (mp) cc_final: 0.7324 (mp) REVERT: E 68 GLU cc_start: 0.8188 (tp30) cc_final: 0.7849 (tp30) outliers start: 100 outliers final: 69 residues processed: 815 average time/residue: 0.4596 time to fit residues: 556.5238 Evaluate side-chains 833 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 750 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 55 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 177 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 310 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26848 Z= 0.226 Angle : 0.647 12.306 36556 Z= 0.329 Chirality : 0.043 0.273 4184 Planarity : 0.004 0.056 4544 Dihedral : 14.605 174.413 4287 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.25 % Allowed : 21.90 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.92 (0.14), residues: 3164 helix: 0.67 (0.16), residues: 1071 sheet: -0.23 (0.28), residues: 336 loop : -1.56 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 33 HIS 0.017 0.001 HIS B 132 PHE 0.015 0.001 PHE C1221 TYR 0.022 0.002 TYR D 165 ARG 0.010 0.001 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 770 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7927 (mtpp) REVERT: A 45 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7350 (mtp85) REVERT: A 68 TYR cc_start: 0.8541 (m-10) cc_final: 0.8132 (m-10) REVERT: A 102 LEU cc_start: 0.8276 (tp) cc_final: 0.7940 (tp) REVERT: A 118 ASP cc_start: 0.7876 (p0) cc_final: 0.7387 (p0) REVERT: A 120 ASP cc_start: 0.7826 (p0) cc_final: 0.7302 (p0) REVERT: A 153 VAL cc_start: 0.8525 (t) cc_final: 0.8226 (p) REVERT: B 33 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7474 (ttp80) REVERT: B 51 MET cc_start: 0.7549 (mmm) cc_final: 0.7338 (mmm) REVERT: B 60 GLU cc_start: 0.6537 (tp30) cc_final: 0.5979 (tp30) REVERT: B 140 ILE cc_start: 0.7751 (tp) cc_final: 0.6980 (tp) REVERT: B 142 MET cc_start: 0.6955 (mmm) cc_final: 0.6261 (mmm) REVERT: B 182 ARG cc_start: 0.7134 (ttt180) cc_final: 0.6762 (ttt180) REVERT: B 186 ASN cc_start: 0.8223 (t0) cc_final: 0.7885 (t0) REVERT: B 188 GLU cc_start: 0.6726 (pm20) cc_final: 0.6115 (mp0) REVERT: B 212 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6382 (p0) REVERT: B 226 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 8 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7324 (mttt) REVERT: C 22 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8169 (mt) REVERT: C 54 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7211 (mtm-85) REVERT: C 99 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7724 (tppt) REVERT: C 124 MET cc_start: 0.7527 (ttp) cc_final: 0.6441 (tmm) REVERT: C 169 LYS cc_start: 0.8076 (tmtt) cc_final: 0.7762 (tmtt) REVERT: C 177 ILE cc_start: 0.8032 (mm) cc_final: 0.7645 (tp) REVERT: C 191 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8321 (mtmm) REVERT: C 197 ARG cc_start: 0.7163 (mtp-110) cc_final: 0.6688 (mtp85) REVERT: C 218 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7658 (tp30) REVERT: C 278 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8065 (pt0) REVERT: C 342 ASP cc_start: 0.7725 (t0) cc_final: 0.7451 (t0) REVERT: C 358 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7704 (t70) REVERT: C 392 GLU cc_start: 0.7680 (tp30) cc_final: 0.7153 (tp30) REVERT: C 427 ASP cc_start: 0.8143 (m-30) cc_final: 0.7809 (m-30) REVERT: C 447 HIS cc_start: 0.7680 (t-170) cc_final: 0.7210 (t-170) REVERT: C 461 GLU cc_start: 0.7937 (tt0) cc_final: 0.7138 (tm-30) REVERT: C 504 GLU cc_start: 0.7574 (pp20) cc_final: 0.7187 (pp20) REVERT: C 515 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5990 (ttt) REVERT: C 541 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7748 (mm-30) REVERT: C 622 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7784 (p0) REVERT: C 623 LEU cc_start: 0.7942 (pp) cc_final: 0.7558 (pp) REVERT: C 668 ILE cc_start: 0.8279 (mm) cc_final: 0.8047 (mt) REVERT: C 674 ASP cc_start: 0.7890 (t0) cc_final: 0.7393 (t0) REVERT: C 719 LYS cc_start: 0.7394 (tptp) cc_final: 0.7154 (mmmt) REVERT: C 737 ASN cc_start: 0.8487 (m-40) cc_final: 0.7527 (m-40) REVERT: C 761 GLN cc_start: 0.7390 (mm110) cc_final: 0.7019 (mp10) REVERT: C 779 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.7832 (ttm-80) REVERT: C 793 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6796 (mt-10) REVERT: C 800 MET cc_start: 0.7516 (ptp) cc_final: 0.7280 (ptm) REVERT: C 820 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: C 825 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7437 (mm-30) REVERT: C 836 LEU cc_start: 0.7452 (mm) cc_final: 0.7136 (mp) REVERT: C 928 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8635 (m) REVERT: C 943 LYS cc_start: 0.8727 (mmpt) cc_final: 0.8459 (mmtm) REVERT: C 951 MET cc_start: 0.8582 (mtp) cc_final: 0.8333 (mtp) REVERT: C 955 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7685 (tp-100) REVERT: C 957 LYS cc_start: 0.9065 (pptt) cc_final: 0.8657 (pptt) REVERT: C 1079 ILE cc_start: 0.8345 (mm) cc_final: 0.7299 (mt) REVERT: C 1107 MET cc_start: 0.6996 (ptm) cc_final: 0.6768 (ptm) REVERT: C 1119 MET cc_start: 0.7726 (tpp) cc_final: 0.7402 (tmm) REVERT: C 1122 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7839 (mmmm) REVERT: C 1146 GLN cc_start: 0.8179 (tp40) cc_final: 0.7603 (tp40) REVERT: C 1164 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: C 1178 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8195 (mmtt) REVERT: C 1192 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7503 (mp0) REVERT: C 1274 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7171 (tp30) REVERT: C 1279 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7019 (mm-30) REVERT: C 1289 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 1290 MET cc_start: 0.7830 (tmm) cc_final: 0.7592 (tmm) REVERT: C 1303 LYS cc_start: 0.8115 (tppp) cc_final: 0.7740 (ttmm) REVERT: C 1315 MET cc_start: 0.5932 (mmp) cc_final: 0.5573 (tpp) REVERT: C 1329 GLU cc_start: 0.7377 (tt0) cc_final: 0.6631 (mt-10) REVERT: C 1340 GLU cc_start: 0.6634 (mp0) cc_final: 0.6357 (mp0) REVERT: D 21 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7239 (mmtp) REVERT: D 35 PHE cc_start: 0.6658 (m-80) cc_final: 0.6366 (m-80) REVERT: D 50 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8461 (tptp) REVERT: D 66 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7902 (mmmm) REVERT: D 69 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7075 (tm-30) REVERT: D 84 ILE cc_start: 0.7883 (pt) cc_final: 0.7654 (mp) REVERT: D 94 GLN cc_start: 0.7132 (tp40) cc_final: 0.6663 (tp40) REVERT: D 104 HIS cc_start: 0.7637 (p-80) cc_final: 0.7284 (p90) REVERT: D 115 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.7938 (m-10) REVERT: D 117 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7636 (mm) REVERT: D 124 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8191 (tt) REVERT: D 141 PHE cc_start: 0.7905 (m-10) cc_final: 0.7472 (m-10) REVERT: D 179 LYS cc_start: 0.8421 (mttt) cc_final: 0.8041 (mmmm) REVERT: D 180 MET cc_start: 0.6623 (ppp) cc_final: 0.6301 (ppp) REVERT: D 183 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 190 LYS cc_start: 0.7960 (ptpp) cc_final: 0.7390 (ptpp) REVERT: D 198 CYS cc_start: 0.8113 (m) cc_final: 0.7423 (p) REVERT: D 200 GLN cc_start: 0.8197 (pp30) cc_final: 0.7556 (pp30) REVERT: D 202 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8175 (mtm-85) REVERT: D 203 GLU cc_start: 0.8575 (pp20) cc_final: 0.8321 (pp20) REVERT: D 211 GLU cc_start: 0.8161 (pp20) cc_final: 0.7636 (pp20) REVERT: D 215 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8297 (mmtt) REVERT: D 216 LYS cc_start: 0.8705 (tppt) cc_final: 0.8301 (mmmm) REVERT: D 222 LYS cc_start: 0.8408 (mptt) cc_final: 0.7966 (mptt) REVERT: D 233 LYS cc_start: 0.8264 (mmmm) cc_final: 0.7967 (mmmm) REVERT: D 236 TRP cc_start: 0.8820 (m-10) cc_final: 0.8511 (m-10) REVERT: D 241 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7740 (p) REVERT: D 278 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7910 (ttm110) REVERT: D 294 ASN cc_start: 0.8189 (t0) cc_final: 0.6843 (t0) REVERT: D 295 GLU cc_start: 0.7904 (tt0) cc_final: 0.7478 (tt0) REVERT: D 297 ARG cc_start: 0.8339 (tmm-80) cc_final: 0.7735 (tmm-80) REVERT: D 298 MET cc_start: 0.7925 (mmp) cc_final: 0.6891 (mmt) REVERT: D 301 GLU cc_start: 0.7915 (tp30) cc_final: 0.7576 (tm-30) REVERT: D 330 MET cc_start: 0.7507 (ttt) cc_final: 0.7115 (ttt) REVERT: D 378 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7882 (mmmm) REVERT: D 398 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8136 (mmmt) REVERT: D 400 MET cc_start: 0.8543 (mtm) cc_final: 0.7826 (mtm) REVERT: D 404 GLU cc_start: 0.7957 (pm20) cc_final: 0.7737 (pp20) REVERT: D 431 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7693 (ttp-110) REVERT: D 432 LEU cc_start: 0.8409 (mm) cc_final: 0.8003 (mm) REVERT: D 479 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7342 (tm-30) REVERT: D 506 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7989 (p) REVERT: D 511 TYR cc_start: 0.7586 (t80) cc_final: 0.7035 (t80) REVERT: D 531 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7873 (ttmm) REVERT: D 566 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7768 (mtpp) REVERT: D 571 ASP cc_start: 0.7629 (p0) cc_final: 0.7411 (p0) REVERT: D 604 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7131 (tmm) REVERT: D 644 MET cc_start: 0.8073 (mpp) cc_final: 0.7658 (mtm) REVERT: D 678 ARG cc_start: 0.8660 (ppt170) cc_final: 0.7985 (ttp80) REVERT: D 681 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7854 (ttpp) REVERT: D 697 MET cc_start: 0.7847 (tmm) cc_final: 0.7510 (tmm) REVERT: D 698 MET cc_start: 0.7669 (tpt) cc_final: 0.7219 (tpp) REVERT: D 702 GLN cc_start: 0.7925 (pt0) cc_final: 0.7565 (pp30) REVERT: D 703 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7380 (m) REVERT: D 715 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7910 (ttmm) REVERT: D 724 MET cc_start: 0.7896 (ttp) cc_final: 0.7646 (mtp) REVERT: D 728 SER cc_start: 0.8162 (p) cc_final: 0.7742 (t) REVERT: D 757 THR cc_start: 0.8478 (t) cc_final: 0.8261 (m) REVERT: D 781 LYS cc_start: 0.8706 (tptp) cc_final: 0.8276 (tppt) REVERT: D 805 GLN cc_start: 0.7820 (pm20) cc_final: 0.7520 (pm20) REVERT: D 806 ASP cc_start: 0.7497 (p0) cc_final: 0.6674 (t0) REVERT: D 808 VAL cc_start: 0.8500 (t) cc_final: 0.8150 (p) REVERT: D 867 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7464 (tm-30) REVERT: D 873 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7891 (mt-10) REVERT: D 877 VAL cc_start: 0.8269 (t) cc_final: 0.7998 (p) REVERT: D 964 LYS cc_start: 0.7970 (tppt) cc_final: 0.7720 (tppt) REVERT: D 992 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7720 (mmtt) REVERT: D 993 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6168 (mm-30) REVERT: D 1007 ASP cc_start: 0.8083 (t70) cc_final: 0.7867 (t0) REVERT: D 1095 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6190 (pmm) REVERT: D 1119 ASP cc_start: 0.7929 (t0) cc_final: 0.7553 (m-30) REVERT: D 1146 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8120 (mm-30) REVERT: D 1189 MET cc_start: 0.7167 (mmp) cc_final: 0.6743 (mmp) REVERT: D 1231 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.6727 (ttm-80) REVERT: D 1232 TYR cc_start: 0.8145 (t80) cc_final: 0.7876 (t80) REVERT: D 1247 LYS cc_start: 0.7834 (ttmt) cc_final: 0.7562 (ttmt) REVERT: D 1291 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8222 (mm-30) REVERT: D 1334 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7426 (mm-30) REVERT: D 1352 ILE cc_start: 0.8361 (tp) cc_final: 0.7966 (tt) REVERT: E 11 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: E 53 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7027 (mm-30) REVERT: E 59 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7400 (mp) REVERT: E 68 GLU cc_start: 0.8170 (tp30) cc_final: 0.7846 (tp30) outliers start: 115 outliers final: 74 residues processed: 819 average time/residue: 0.4552 time to fit residues: 551.5616 Evaluate side-chains 848 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 755 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1286 LYS Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 chunk 185 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 197 optimal weight: 0.0000 chunk 211 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 282 optimal weight: 9.9990 overall best weight: 1.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS C 580 GLN C 824 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26848 Z= 0.313 Angle : 0.727 12.583 36556 Z= 0.372 Chirality : 0.045 0.275 4184 Planarity : 0.005 0.070 4544 Dihedral : 14.714 175.415 4287 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.47 % Allowed : 22.30 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.10 (0.14), residues: 3164 helix: 0.46 (0.16), residues: 1071 sheet: -0.42 (0.27), residues: 359 loop : -1.62 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP D 33 HIS 0.009 0.001 HIS C1023 PHE 0.026 0.002 PHE C 514 TYR 0.027 0.002 TYR D 165 ARG 0.011 0.001 ARG D1369 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 788 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7947 (mtpp) REVERT: A 33 ARG cc_start: 0.8097 (tpt90) cc_final: 0.7740 (mmm160) REVERT: A 45 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7251 (mtp85) REVERT: A 58 GLU cc_start: 0.7665 (tt0) cc_final: 0.7145 (tt0) REVERT: A 67 GLU cc_start: 0.7756 (tp30) cc_final: 0.7497 (tp30) REVERT: A 80 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 102 LEU cc_start: 0.8234 (tp) cc_final: 0.7905 (tp) REVERT: A 118 ASP cc_start: 0.7918 (p0) cc_final: 0.7442 (p0) REVERT: A 120 ASP cc_start: 0.7855 (p0) cc_final: 0.7531 (p0) REVERT: A 122 GLU cc_start: 0.7582 (pm20) cc_final: 0.7318 (pm20) REVERT: A 153 VAL cc_start: 0.8524 (t) cc_final: 0.8239 (p) REVERT: A 170 ARG cc_start: 0.6541 (ptt180) cc_final: 0.6264 (ptt180) REVERT: A 181 GLU cc_start: 0.6967 (mp0) cc_final: 0.6668 (mp0) REVERT: B 33 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7508 (ttp80) REVERT: B 60 GLU cc_start: 0.6735 (tp30) cc_final: 0.6166 (tp30) REVERT: B 71 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7655 (mmmt) REVERT: B 142 MET cc_start: 0.6870 (mmm) cc_final: 0.6595 (mmm) REVERT: B 182 ARG cc_start: 0.7291 (ttt180) cc_final: 0.6987 (ttt180) REVERT: B 186 ASN cc_start: 0.8229 (t0) cc_final: 0.7977 (t0) REVERT: B 188 GLU cc_start: 0.6796 (pm20) cc_final: 0.6235 (mp0) REVERT: B 212 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6531 (p0) REVERT: B 226 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 8 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7382 (mttt) REVERT: C 22 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8166 (mt) REVERT: C 33 ASP cc_start: 0.6519 (p0) cc_final: 0.6300 (p0) REVERT: C 50 GLU cc_start: 0.7365 (tp30) cc_final: 0.6492 (tp30) REVERT: C 54 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.7046 (mtt180) REVERT: C 99 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7766 (tppt) REVERT: C 124 MET cc_start: 0.7580 (ttp) cc_final: 0.6408 (tmm) REVERT: C 169 LYS cc_start: 0.8109 (tmtt) cc_final: 0.7782 (tmtt) REVERT: C 177 ILE cc_start: 0.8136 (mm) cc_final: 0.7726 (tp) REVERT: C 187 GLU cc_start: 0.7169 (pt0) cc_final: 0.6859 (pt0) REVERT: C 191 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8344 (mtmm) REVERT: C 197 ARG cc_start: 0.7090 (mtp-110) cc_final: 0.6572 (mtp85) REVERT: C 215 TYR cc_start: 0.7862 (m-80) cc_final: 0.7586 (m-80) REVERT: C 218 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7721 (tp30) REVERT: C 275 ARG cc_start: 0.9032 (mmm160) cc_final: 0.8559 (mmm-85) REVERT: C 300 ASP cc_start: 0.6666 (m-30) cc_final: 0.6461 (m-30) REVERT: C 342 ASP cc_start: 0.7794 (t0) cc_final: 0.7560 (t0) REVERT: C 358 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7755 (t70) REVERT: C 392 GLU cc_start: 0.7772 (tp30) cc_final: 0.7238 (tp30) REVERT: C 447 HIS cc_start: 0.7734 (t-170) cc_final: 0.7251 (t-170) REVERT: C 461 GLU cc_start: 0.7876 (tt0) cc_final: 0.7120 (tm-30) REVERT: C 504 GLU cc_start: 0.7448 (pp20) cc_final: 0.7120 (pp20) REVERT: C 515 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5873 (ttt) REVERT: C 541 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7706 (mm-30) REVERT: C 622 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7869 (p0) REVERT: C 623 LEU cc_start: 0.7885 (pp) cc_final: 0.7529 (pp) REVERT: C 668 ILE cc_start: 0.8267 (mm) cc_final: 0.8053 (mt) REVERT: C 674 ASP cc_start: 0.7932 (t0) cc_final: 0.7431 (t0) REVERT: C 719 LYS cc_start: 0.7427 (tptp) cc_final: 0.7186 (mmmt) REVERT: C 737 ASN cc_start: 0.8406 (m-40) cc_final: 0.7533 (m-40) REVERT: C 761 GLN cc_start: 0.7375 (mm110) cc_final: 0.7074 (mp10) REVERT: C 779 ARG cc_start: 0.8289 (ttt-90) cc_final: 0.7796 (ttm-80) REVERT: C 793 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6723 (mt-10) REVERT: C 800 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7262 (ptm) REVERT: C 820 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: C 825 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7459 (mm-30) REVERT: C 864 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7493 (mmtp) REVERT: C 928 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8595 (m) REVERT: C 943 LYS cc_start: 0.8652 (mmpt) cc_final: 0.8370 (mmmt) REVERT: C 951 MET cc_start: 0.8554 (mtp) cc_final: 0.8247 (mtp) REVERT: C 954 LYS cc_start: 0.8482 (mtmm) cc_final: 0.7818 (mtmm) REVERT: C 955 GLN cc_start: 0.8375 (tp-100) cc_final: 0.7720 (tp-100) REVERT: C 957 LYS cc_start: 0.9082 (pptt) cc_final: 0.8680 (pptt) REVERT: C 1030 GLU cc_start: 0.8630 (tp30) cc_final: 0.8317 (tp30) REVERT: C 1107 MET cc_start: 0.7100 (ptm) cc_final: 0.6858 (ptm) REVERT: C 1119 MET cc_start: 0.7833 (tpp) cc_final: 0.7415 (tmm) REVERT: C 1122 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7899 (mmmm) REVERT: C 1142 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7827 (mtt-85) REVERT: C 1146 GLN cc_start: 0.8266 (tp40) cc_final: 0.7709 (tp40) REVERT: C 1150 ASP cc_start: 0.7637 (t70) cc_final: 0.7390 (t70) REVERT: C 1164 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: C 1192 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7519 (mp0) REVERT: C 1265 PHE cc_start: 0.6704 (t80) cc_final: 0.6457 (t80) REVERT: C 1274 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7268 (tp30) REVERT: C 1279 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6973 (mm-30) REVERT: C 1289 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 1290 MET cc_start: 0.7963 (tmm) cc_final: 0.7627 (tmm) REVERT: C 1303 LYS cc_start: 0.8084 (tppp) cc_final: 0.7677 (ttmm) REVERT: C 1329 GLU cc_start: 0.7241 (tt0) cc_final: 0.6524 (mt-10) REVERT: C 1332 SER cc_start: 0.7930 (p) cc_final: 0.7616 (p) REVERT: D 21 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7306 (mmtt) REVERT: D 35 PHE cc_start: 0.6712 (m-80) cc_final: 0.6376 (m-80) REVERT: D 50 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8439 (tptp) REVERT: D 66 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7991 (mmmm) REVERT: D 69 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7216 (tm-30) REVERT: D 84 ILE cc_start: 0.7850 (pt) cc_final: 0.7647 (mp) REVERT: D 94 GLN cc_start: 0.7345 (tp40) cc_final: 0.6998 (tp40) REVERT: D 104 HIS cc_start: 0.7644 (p-80) cc_final: 0.7234 (p90) REVERT: D 115 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.8044 (m-10) REVERT: D 117 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7635 (mm) REVERT: D 124 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8307 (tt) REVERT: D 130 MET cc_start: 0.7644 (mmt) cc_final: 0.7415 (mmm) REVERT: D 141 PHE cc_start: 0.7930 (m-10) cc_final: 0.7393 (m-10) REVERT: D 179 LYS cc_start: 0.8474 (mttt) cc_final: 0.8035 (mmmm) REVERT: D 180 MET cc_start: 0.6658 (ppp) cc_final: 0.6356 (ppp) REVERT: D 183 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7963 (tm-30) REVERT: D 186 GLN cc_start: 0.7652 (tt0) cc_final: 0.7116 (tt0) REVERT: D 190 LYS cc_start: 0.8030 (ptpp) cc_final: 0.7384 (ptpp) REVERT: D 198 CYS cc_start: 0.8175 (m) cc_final: 0.7846 (m) REVERT: D 200 GLN cc_start: 0.8249 (pp30) cc_final: 0.7766 (pp30) REVERT: D 202 ARG cc_start: 0.8570 (mtm110) cc_final: 0.8264 (mtm-85) REVERT: D 211 GLU cc_start: 0.8170 (pp20) cc_final: 0.7694 (pp20) REVERT: D 215 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8265 (mmtt) REVERT: D 219 LYS cc_start: 0.8539 (mttt) cc_final: 0.8194 (mttt) REVERT: D 222 LYS cc_start: 0.8429 (mptt) cc_final: 0.7997 (mptt) REVERT: D 233 LYS cc_start: 0.8281 (mmmm) cc_final: 0.8013 (mmmm) REVERT: D 278 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7905 (ttm110) REVERT: D 294 ASN cc_start: 0.8190 (t0) cc_final: 0.6846 (t0) REVERT: D 295 GLU cc_start: 0.7936 (tt0) cc_final: 0.7530 (tt0) REVERT: D 297 ARG cc_start: 0.8346 (tmm-80) cc_final: 0.7763 (tmm-80) REVERT: D 298 MET cc_start: 0.8072 (mmp) cc_final: 0.7039 (mmt) REVERT: D 301 GLU cc_start: 0.7906 (tp30) cc_final: 0.7590 (tm-30) REVERT: D 330 MET cc_start: 0.7553 (ttt) cc_final: 0.7030 (ttt) REVERT: D 339 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.7377 (ptm160) REVERT: D 378 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7980 (mmmt) REVERT: D 398 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8202 (mmmt) REVERT: D 400 MET cc_start: 0.8548 (mtm) cc_final: 0.7848 (mtm) REVERT: D 403 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7929 (ttm110) REVERT: D 412 LEU cc_start: 0.8027 (tt) cc_final: 0.7530 (tp) REVERT: D 432 LEU cc_start: 0.8443 (mm) cc_final: 0.8050 (mm) REVERT: D 479 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7326 (pp20) REVERT: D 485 MET cc_start: 0.7623 (mmm) cc_final: 0.7164 (tpp) REVERT: D 506 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8098 (p) REVERT: D 511 TYR cc_start: 0.7671 (t80) cc_final: 0.7122 (t80) REVERT: D 513 MET cc_start: 0.7926 (tpt) cc_final: 0.7635 (tpp) REVERT: D 531 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8060 (ttmm) REVERT: D 556 GLU cc_start: 0.6615 (tp30) cc_final: 0.6186 (tp30) REVERT: D 566 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7686 (mtpp) REVERT: D 571 ASP cc_start: 0.7625 (p0) cc_final: 0.7371 (p0) REVERT: D 589 TYR cc_start: 0.8774 (t80) cc_final: 0.8426 (t80) REVERT: D 604 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7128 (tmm) REVERT: D 644 MET cc_start: 0.8012 (mpp) cc_final: 0.7694 (mtm) REVERT: D 678 ARG cc_start: 0.8667 (ppt170) cc_final: 0.7996 (ttp80) REVERT: D 681 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7862 (ttpp) REVERT: D 697 MET cc_start: 0.7806 (tmm) cc_final: 0.7505 (tmm) REVERT: D 698 MET cc_start: 0.7719 (tpt) cc_final: 0.7336 (tpp) REVERT: D 715 LYS cc_start: 0.8247 (ttmm) cc_final: 0.8001 (ttmm) REVERT: D 728 SER cc_start: 0.8138 (p) cc_final: 0.7831 (t) REVERT: D 739 GLN cc_start: 0.7910 (tt0) cc_final: 0.7268 (tp40) REVERT: D 781 LYS cc_start: 0.8705 (tptp) cc_final: 0.8295 (tppt) REVERT: D 805 GLN cc_start: 0.7856 (pm20) cc_final: 0.7540 (pm20) REVERT: D 806 ASP cc_start: 0.7516 (p0) cc_final: 0.6699 (t0) REVERT: D 808 VAL cc_start: 0.8528 (t) cc_final: 0.8206 (p) REVERT: D 811 GLU cc_start: 0.7654 (tp30) cc_final: 0.7317 (tp30) REVERT: D 867 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7524 (tm-30) REVERT: D 877 VAL cc_start: 0.8341 (t) cc_final: 0.8083 (p) REVERT: D 964 LYS cc_start: 0.7994 (tppt) cc_final: 0.7750 (tppt) REVERT: D 992 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7683 (mmtt) REVERT: D 993 GLU cc_start: 0.6225 (mm-30) cc_final: 0.5997 (mm-30) REVERT: D 1025 MET cc_start: 0.6930 (tpt) cc_final: 0.6563 (ppp) REVERT: D 1040 MET cc_start: 0.6678 (tpp) cc_final: 0.4307 (mmm) REVERT: D 1095 MET cc_start: 0.6571 (pmm) cc_final: 0.6280 (pmm) REVERT: D 1101 LEU cc_start: 0.8630 (tp) cc_final: 0.7956 (pp) REVERT: D 1119 ASP cc_start: 0.7846 (t0) cc_final: 0.7500 (m-30) REVERT: D 1146 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8174 (mm-30) REVERT: D 1189 MET cc_start: 0.7208 (mmp) cc_final: 0.6762 (mmp) REVERT: D 1244 GLN cc_start: 0.8349 (tt0) cc_final: 0.7686 (tm-30) REVERT: D 1247 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7414 (ttpt) REVERT: D 1291 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8232 (mm-30) REVERT: D 1334 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7510 (mm-30) REVERT: D 1352 ILE cc_start: 0.8407 (tp) cc_final: 0.8027 (tt) REVERT: E 11 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: E 53 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7031 (mm-30) REVERT: E 59 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7457 (mp) REVERT: E 68 GLU cc_start: 0.8186 (tp30) cc_final: 0.7767 (tp30) outliers start: 121 outliers final: 80 residues processed: 837 average time/residue: 0.4471 time to fit residues: 555.7829 Evaluate side-chains 869 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 772 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1286 LYS Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.0270 chunk 271 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 273 optimal weight: 0.5980 chunk 288 optimal weight: 0.0000 chunk 189 optimal weight: 5.9990 overall best weight: 0.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 824 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26848 Z= 0.192 Angle : 0.706 15.846 36556 Z= 0.354 Chirality : 0.044 0.224 4184 Planarity : 0.004 0.058 4544 Dihedral : 14.613 174.131 4287 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.62 % Allowed : 23.82 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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 (0.15), residues: 3164 helix: 0.54 (0.16), residues: 1077 sheet: -0.21 (0.27), residues: 359 loop : -1.53 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 33 HIS 0.014 0.001 HIS B 132 PHE 0.025 0.001 PHE C 514 TYR 0.028 0.002 TYR D 165 ARG 0.009 0.001 ARG D1369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 766 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7924 (mtpp) REVERT: A 58 GLU cc_start: 0.7607 (tt0) cc_final: 0.7070 (tt0) REVERT: A 67 GLU cc_start: 0.7730 (tp30) cc_final: 0.7159 (tp30) REVERT: A 68 TYR cc_start: 0.8563 (m-10) cc_final: 0.8098 (m-10) REVERT: A 102 LEU cc_start: 0.8221 (tp) cc_final: 0.7920 (tp) REVERT: A 118 ASP cc_start: 0.7892 (p0) cc_final: 0.7446 (p0) REVERT: A 120 ASP cc_start: 0.7806 (p0) cc_final: 0.7282 (p0) REVERT: A 122 GLU cc_start: 0.7595 (pm20) cc_final: 0.7392 (pm20) REVERT: A 153 VAL cc_start: 0.8516 (t) cc_final: 0.8202 (p) REVERT: A 206 GLU cc_start: 0.7305 (pp20) cc_final: 0.6501 (tm-30) REVERT: B 33 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7469 (ttp80) REVERT: B 44 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7827 (ttm110) REVERT: B 60 GLU cc_start: 0.6707 (tp30) cc_final: 0.6150 (tp30) REVERT: B 71 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7629 (mmmt) REVERT: B 142 MET cc_start: 0.6815 (mmm) cc_final: 0.6544 (mmm) REVERT: B 182 ARG cc_start: 0.7210 (ttt180) cc_final: 0.6879 (ttt180) REVERT: B 212 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6433 (p0) REVERT: C 8 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7350 (mttt) REVERT: C 22 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8103 (mt) REVERT: C 50 GLU cc_start: 0.7212 (tp30) cc_final: 0.6330 (tp30) REVERT: C 54 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7005 (mtt180) REVERT: C 99 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7755 (tppt) REVERT: C 124 MET cc_start: 0.7495 (ttp) cc_final: 0.6381 (tmm) REVERT: C 151 ARG cc_start: 0.6903 (mmm-85) cc_final: 0.5951 (tmm-80) REVERT: C 169 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7750 (tmtt) REVERT: C 191 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8321 (mtmm) REVERT: C 197 ARG cc_start: 0.7168 (mtp-110) cc_final: 0.6692 (mtp85) REVERT: C 218 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7579 (tp30) REVERT: C 275 ARG cc_start: 0.9009 (mmm160) cc_final: 0.8656 (mmm160) REVERT: C 300 ASP cc_start: 0.6780 (m-30) cc_final: 0.6577 (m-30) REVERT: C 342 ASP cc_start: 0.7732 (t0) cc_final: 0.7438 (t0) REVERT: C 392 GLU cc_start: 0.7632 (tp30) cc_final: 0.7123 (tp30) REVERT: C 394 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7266 (ttm110) REVERT: C 447 HIS cc_start: 0.7714 (t-170) cc_final: 0.7229 (t-170) REVERT: C 461 GLU cc_start: 0.7874 (tt0) cc_final: 0.7101 (tm-30) REVERT: C 504 GLU cc_start: 0.7526 (pp20) cc_final: 0.7153 (pp20) REVERT: C 515 MET cc_start: 0.6343 (ttt) cc_final: 0.5863 (ttt) REVERT: C 541 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 602 GLU cc_start: 0.6623 (pp20) cc_final: 0.6098 (pp20) REVERT: C 622 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7822 (p0) REVERT: C 623 LEU cc_start: 0.7836 (pp) cc_final: 0.7407 (pp) REVERT: C 626 GLU cc_start: 0.8483 (mp0) cc_final: 0.7959 (mp0) REVERT: C 668 ILE cc_start: 0.8246 (mm) cc_final: 0.8037 (mt) REVERT: C 674 ASP cc_start: 0.7830 (t0) cc_final: 0.7361 (t0) REVERT: C 719 LYS cc_start: 0.7337 (tptp) cc_final: 0.7122 (mmmt) REVERT: C 737 ASN cc_start: 0.8396 (m-40) cc_final: 0.7505 (m-40) REVERT: C 761 GLN cc_start: 0.7332 (mm110) cc_final: 0.6848 (mp10) REVERT: C 779 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.7754 (ttm-80) REVERT: C 793 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6742 (mt-10) REVERT: C 800 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6996 (ptm) REVERT: C 820 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: C 825 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7378 (mm-30) REVERT: C 864 LYS cc_start: 0.7639 (mmtp) cc_final: 0.7212 (mmtp) REVERT: C 886 LYS cc_start: 0.7437 (tmtt) cc_final: 0.7131 (tmtt) REVERT: C 928 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8618 (m) REVERT: C 943 LYS cc_start: 0.8629 (mmpt) cc_final: 0.8403 (mmmt) REVERT: C 955 GLN cc_start: 0.8401 (tp-100) cc_final: 0.7730 (tp-100) REVERT: C 957 LYS cc_start: 0.9020 (pptt) cc_final: 0.8625 (pptt) REVERT: C 1025 PHE cc_start: 0.7626 (m-80) cc_final: 0.7252 (m-80) REVERT: C 1030 GLU cc_start: 0.8544 (tp30) cc_final: 0.8279 (tp30) REVERT: C 1047 LEU cc_start: 0.8431 (mp) cc_final: 0.8060 (mt) REVERT: C 1056 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8061 (m) REVERT: C 1080 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7891 (t0) REVERT: C 1107 MET cc_start: 0.6983 (ptm) cc_final: 0.6715 (ptm) REVERT: C 1119 MET cc_start: 0.7648 (tpp) cc_final: 0.7393 (tmm) REVERT: C 1122 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7839 (mmmm) REVERT: C 1146 GLN cc_start: 0.8146 (tp40) cc_final: 0.7551 (tp40) REVERT: C 1219 GLU cc_start: 0.7460 (pm20) cc_final: 0.7240 (pm20) REVERT: C 1279 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6934 (mm-30) REVERT: C 1289 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 1290 MET cc_start: 0.7878 (tmm) cc_final: 0.7671 (tmm) REVERT: C 1303 LYS cc_start: 0.8005 (tppp) cc_final: 0.7682 (ttmm) REVERT: C 1315 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.5707 (mmp) REVERT: D 21 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7078 (mmmm) REVERT: D 35 PHE cc_start: 0.6651 (m-80) cc_final: 0.6389 (m-80) REVERT: D 50 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8441 (tptp) REVERT: D 66 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7851 (mmmm) REVERT: D 69 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7134 (tm-30) REVERT: D 84 ILE cc_start: 0.7838 (pt) cc_final: 0.7627 (mp) REVERT: D 94 GLN cc_start: 0.7186 (tp40) cc_final: 0.6840 (tp40) REVERT: D 104 HIS cc_start: 0.7629 (p-80) cc_final: 0.7294 (p90) REVERT: D 115 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.7977 (m-10) REVERT: D 117 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7546 (mm) REVERT: D 124 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8204 (tt) REVERT: D 130 MET cc_start: 0.7583 (mmt) cc_final: 0.7366 (mmm) REVERT: D 141 PHE cc_start: 0.7902 (m-10) cc_final: 0.7389 (m-10) REVERT: D 179 LYS cc_start: 0.8388 (mttt) cc_final: 0.7939 (mmmm) REVERT: D 180 MET cc_start: 0.6729 (ppp) cc_final: 0.6418 (ppp) REVERT: D 183 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 186 GLN cc_start: 0.7714 (tt0) cc_final: 0.7212 (tt0) REVERT: D 190 LYS cc_start: 0.7904 (ptpp) cc_final: 0.7256 (ptpp) REVERT: D 200 GLN cc_start: 0.8265 (pp30) cc_final: 0.7660 (pp30) REVERT: D 202 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8299 (mtm-85) REVERT: D 203 GLU cc_start: 0.8557 (pp20) cc_final: 0.8226 (pp20) REVERT: D 211 GLU cc_start: 0.8122 (pp20) cc_final: 0.7585 (pp20) REVERT: D 215 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8234 (mmtt) REVERT: D 216 LYS cc_start: 0.8698 (tppt) cc_final: 0.8312 (mmmm) REVERT: D 222 LYS cc_start: 0.8403 (mptt) cc_final: 0.7942 (mptt) REVERT: D 233 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7956 (mmmm) REVERT: D 236 TRP cc_start: 0.8859 (m-10) cc_final: 0.8561 (m-10) REVERT: D 278 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7906 (ttm110) REVERT: D 294 ASN cc_start: 0.8197 (t0) cc_final: 0.6855 (t0) REVERT: D 295 GLU cc_start: 0.7943 (tt0) cc_final: 0.7502 (tt0) REVERT: D 297 ARG cc_start: 0.8293 (tmm-80) cc_final: 0.7692 (tmm-80) REVERT: D 298 MET cc_start: 0.8017 (mmp) cc_final: 0.6988 (mmt) REVERT: D 301 GLU cc_start: 0.7895 (tp30) cc_final: 0.7560 (tm-30) REVERT: D 378 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7804 (mmmm) REVERT: D 398 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8120 (mmmt) REVERT: D 400 MET cc_start: 0.8585 (mtm) cc_final: 0.7858 (mtm) REVERT: D 432 LEU cc_start: 0.8435 (mm) cc_final: 0.8049 (mm) REVERT: D 479 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 506 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7980 (p) REVERT: D 511 TYR cc_start: 0.7544 (t80) cc_final: 0.6877 (t80) REVERT: D 513 MET cc_start: 0.7853 (tpt) cc_final: 0.7559 (tpp) REVERT: D 531 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8014 (ttmm) REVERT: D 556 GLU cc_start: 0.6619 (tp30) cc_final: 0.6314 (tp30) REVERT: D 566 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7626 (mtpp) REVERT: D 568 SER cc_start: 0.7562 (m) cc_final: 0.7128 (t) REVERT: D 571 ASP cc_start: 0.7590 (p0) cc_final: 0.7333 (p0) REVERT: D 589 TYR cc_start: 0.8725 (t80) cc_final: 0.8471 (t80) REVERT: D 604 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7098 (tmm) REVERT: D 644 MET cc_start: 0.7937 (mpp) cc_final: 0.7641 (mtm) REVERT: D 678 ARG cc_start: 0.8638 (ppt170) cc_final: 0.7890 (ttp80) REVERT: D 681 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7852 (ttpp) REVERT: D 698 MET cc_start: 0.7679 (tpt) cc_final: 0.7011 (tmm) REVERT: D 702 GLN cc_start: 0.8079 (pt0) cc_final: 0.7692 (pt0) REVERT: D 715 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7983 (ttmm) REVERT: D 728 SER cc_start: 0.8064 (p) cc_final: 0.7600 (m) REVERT: D 781 LYS cc_start: 0.8652 (tptp) cc_final: 0.8234 (tppt) REVERT: D 805 GLN cc_start: 0.7908 (pm20) cc_final: 0.7554 (pm20) REVERT: D 806 ASP cc_start: 0.7512 (p0) cc_final: 0.6653 (t70) REVERT: D 808 VAL cc_start: 0.8493 (t) cc_final: 0.8153 (p) REVERT: D 811 GLU cc_start: 0.7672 (tp30) cc_final: 0.7362 (tp30) REVERT: D 838 ARG cc_start: 0.7819 (tpt-90) cc_final: 0.7505 (mmm-85) REVERT: D 867 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7444 (tm-30) REVERT: D 877 VAL cc_start: 0.8323 (t) cc_final: 0.8043 (p) REVERT: D 913 GLU cc_start: 0.7886 (tp30) cc_final: 0.7548 (tp30) REVERT: D 964 LYS cc_start: 0.7975 (tppt) cc_final: 0.7720 (tppt) REVERT: D 983 LYS cc_start: 0.7767 (pttm) cc_final: 0.7541 (mppt) REVERT: D 992 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7664 (mmtt) REVERT: D 993 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5905 (mm-30) REVERT: D 1007 ASP cc_start: 0.8118 (t70) cc_final: 0.7882 (t0) REVERT: D 1040 MET cc_start: 0.6591 (tpp) cc_final: 0.4335 (mmm) REVERT: D 1095 MET cc_start: 0.6557 (pmm) cc_final: 0.6228 (pmm) REVERT: D 1101 LEU cc_start: 0.8633 (tp) cc_final: 0.7920 (pp) REVERT: D 1119 ASP cc_start: 0.7941 (t0) cc_final: 0.7585 (m-30) REVERT: D 1146 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8030 (mm-30) REVERT: D 1189 MET cc_start: 0.7178 (mmp) cc_final: 0.6686 (mmp) REVERT: D 1244 GLN cc_start: 0.8300 (tt0) cc_final: 0.7593 (tm-30) REVERT: D 1247 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7406 (ttpt) REVERT: D 1291 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8187 (mm-30) REVERT: D 1334 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7390 (mm-30) REVERT: D 1352 ILE cc_start: 0.8364 (tp) cc_final: 0.7940 (tt) REVERT: E 11 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: E 53 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7050 (mm-30) REVERT: E 59 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7407 (mp) REVERT: E 68 GLU cc_start: 0.8226 (tp30) cc_final: 0.7833 (tp30) outliers start: 98 outliers final: 68 residues processed: 806 average time/residue: 0.4575 time to fit residues: 541.4602 Evaluate side-chains 842 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 757 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1255 VAL 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 3 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 212 optimal weight: 0.0970 chunk 320 optimal weight: 0.8980 chunk 295 optimal weight: 0.0770 chunk 255 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 147 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26848 Z= 0.197 Angle : 0.719 14.021 36556 Z= 0.358 Chirality : 0.043 0.199 4184 Planarity : 0.004 0.058 4544 Dihedral : 14.560 173.376 4287 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.10 % Allowed : 25.04 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.84 (0.15), residues: 3164 helix: 0.60 (0.16), residues: 1071 sheet: -0.02 (0.28), residues: 338 loop : -1.45 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 33 HIS 0.008 0.001 HIS C1023 PHE 0.036 0.001 PHE D1325 TYR 0.025 0.001 TYR D 165 ARG 0.013 0.001 ARG A 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 756 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6500 (tm-30) REVERT: A 25 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7636 (mtpp) REVERT: A 33 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7697 (mmm160) REVERT: A 45 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7292 (mtp-110) REVERT: A 58 GLU cc_start: 0.7602 (tt0) cc_final: 0.7094 (tt0) REVERT: A 67 GLU cc_start: 0.7741 (tp30) cc_final: 0.7080 (tp30) REVERT: A 68 TYR cc_start: 0.8532 (m-10) cc_final: 0.8256 (m-80) REVERT: A 102 LEU cc_start: 0.8213 (tp) cc_final: 0.7914 (tp) REVERT: A 118 ASP cc_start: 0.7878 (p0) cc_final: 0.7427 (p0) REVERT: A 120 ASP cc_start: 0.7795 (p0) cc_final: 0.7304 (p0) REVERT: A 122 GLU cc_start: 0.7601 (pm20) cc_final: 0.7348 (pm20) REVERT: A 153 VAL cc_start: 0.8485 (t) cc_final: 0.8193 (p) REVERT: A 170 ARG cc_start: 0.6435 (ptt180) cc_final: 0.6124 (ptt180) REVERT: B 33 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7441 (ttp80) REVERT: B 44 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7911 (ttm110) REVERT: B 60 GLU cc_start: 0.6702 (tp30) cc_final: 0.6140 (tp30) REVERT: B 71 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7613 (mmmt) REVERT: B 142 MET cc_start: 0.6792 (mmm) cc_final: 0.6500 (mmm) REVERT: B 182 ARG cc_start: 0.7245 (ttt180) cc_final: 0.6866 (ttt180) REVERT: B 212 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6338 (p0) REVERT: C 8 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7354 (mttt) REVERT: C 22 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8062 (mt) REVERT: C 33 ASP cc_start: 0.6432 (p0) cc_final: 0.6223 (p0) REVERT: C 50 GLU cc_start: 0.7161 (tp30) cc_final: 0.6706 (tp30) REVERT: C 54 ARG cc_start: 0.7535 (mtm-85) cc_final: 0.7099 (mtm-85) REVERT: C 99 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7726 (tppt) REVERT: C 124 MET cc_start: 0.7446 (ttp) cc_final: 0.6360 (tmm) REVERT: C 151 ARG cc_start: 0.6870 (mmm-85) cc_final: 0.5953 (tmm-80) REVERT: C 169 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7849 (tmtt) REVERT: C 191 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8328 (mtmm) REVERT: C 197 ARG cc_start: 0.7067 (mtp-110) cc_final: 0.6602 (mtp85) REVERT: C 218 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7567 (tp30) REVERT: C 275 ARG cc_start: 0.8965 (mmm160) cc_final: 0.8730 (mmm160) REVERT: C 299 LYS cc_start: 0.8081 (ptmt) cc_final: 0.7239 (ptmm) REVERT: C 342 ASP cc_start: 0.7716 (t0) cc_final: 0.7462 (t0) REVERT: C 392 GLU cc_start: 0.7563 (tp30) cc_final: 0.7058 (tp30) REVERT: C 394 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7250 (ttm110) REVERT: C 403 MET cc_start: 0.7390 (ttm) cc_final: 0.7107 (ttp) REVERT: C 427 ASP cc_start: 0.8013 (m-30) cc_final: 0.7671 (m-30) REVERT: C 447 HIS cc_start: 0.7707 (t-170) cc_final: 0.7310 (t-170) REVERT: C 461 GLU cc_start: 0.7859 (tt0) cc_final: 0.7071 (tm-30) REVERT: C 504 GLU cc_start: 0.7545 (pp20) cc_final: 0.7153 (pp20) REVERT: C 515 MET cc_start: 0.6355 (ttt) cc_final: 0.5817 (ttt) REVERT: C 540 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7479 (mtm110) REVERT: C 541 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7540 (mm-30) REVERT: C 602 GLU cc_start: 0.6643 (pp20) cc_final: 0.6131 (pp20) REVERT: C 622 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7778 (p0) REVERT: C 623 LEU cc_start: 0.7818 (pp) cc_final: 0.7444 (pp) REVERT: C 626 GLU cc_start: 0.8448 (mp0) cc_final: 0.7899 (mp0) REVERT: C 668 ILE cc_start: 0.8258 (mm) cc_final: 0.8039 (mt) REVERT: C 674 ASP cc_start: 0.7836 (t0) cc_final: 0.7337 (t0) REVERT: C 711 ASP cc_start: 0.7424 (t0) cc_final: 0.7167 (t0) REVERT: C 719 LYS cc_start: 0.7303 (tptp) cc_final: 0.7052 (mmmt) REVERT: C 737 ASN cc_start: 0.8404 (m-40) cc_final: 0.7549 (m110) REVERT: C 761 GLN cc_start: 0.7414 (mm110) cc_final: 0.6813 (mp10) REVERT: C 775 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 779 ARG cc_start: 0.8251 (ttt-90) cc_final: 0.7770 (ttm-80) REVERT: C 793 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6764 (mt-10) REVERT: C 800 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7076 (ptm) REVERT: C 820 GLU cc_start: 0.7627 (tt0) cc_final: 0.7377 (mm-30) REVERT: C 825 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 864 LYS cc_start: 0.7648 (mmtp) cc_final: 0.7266 (mmtp) REVERT: C 886 LYS cc_start: 0.7412 (tmtt) cc_final: 0.7112 (tmtt) REVERT: C 943 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8369 (mmmt) REVERT: C 955 GLN cc_start: 0.8375 (tp-100) cc_final: 0.7699 (tp-100) REVERT: C 957 LYS cc_start: 0.9032 (pptt) cc_final: 0.8626 (pptt) REVERT: C 1025 PHE cc_start: 0.7593 (m-80) cc_final: 0.7261 (m-80) REVERT: C 1047 LEU cc_start: 0.8428 (mp) cc_final: 0.8103 (mm) REVERT: C 1056 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8088 (m) REVERT: C 1080 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.7908 (t0) REVERT: C 1095 ASP cc_start: 0.7250 (m-30) cc_final: 0.6856 (t0) REVERT: C 1107 MET cc_start: 0.6986 (ptm) cc_final: 0.6740 (ptm) REVERT: C 1119 MET cc_start: 0.7445 (tpp) cc_final: 0.7238 (tmm) REVERT: C 1122 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7841 (mmmm) REVERT: C 1146 GLN cc_start: 0.8155 (tp40) cc_final: 0.7810 (tp40) REVERT: C 1160 ASP cc_start: 0.7693 (p0) cc_final: 0.7450 (p0) REVERT: C 1219 GLU cc_start: 0.7365 (pm20) cc_final: 0.7164 (pm20) REVERT: C 1279 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6945 (mm-30) REVERT: C 1289 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 1315 MET cc_start: 0.5586 (OUTLIER) cc_final: 0.5256 (mmp) REVERT: D 21 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7139 (mmmm) REVERT: D 35 PHE cc_start: 0.6692 (m-80) cc_final: 0.6420 (m-80) REVERT: D 50 LYS cc_start: 0.8871 (tmtt) cc_final: 0.8627 (tmtt) REVERT: D 69 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7136 (tm-30) REVERT: D 84 ILE cc_start: 0.7872 (pt) cc_final: 0.7599 (mp) REVERT: D 94 GLN cc_start: 0.7149 (tp40) cc_final: 0.6859 (tp40) REVERT: D 104 HIS cc_start: 0.7647 (p-80) cc_final: 0.7397 (p90) REVERT: D 115 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: D 117 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7518 (mm) REVERT: D 124 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8151 (tt) REVERT: D 130 MET cc_start: 0.7483 (mmt) cc_final: 0.7277 (mmm) REVERT: D 133 ARG cc_start: 0.6843 (ttp80) cc_final: 0.6578 (ttp80) REVERT: D 144 TYR cc_start: 0.7220 (m-10) cc_final: 0.7007 (m-10) REVERT: D 179 LYS cc_start: 0.8304 (mttt) cc_final: 0.7852 (mmmm) REVERT: D 183 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 190 LYS cc_start: 0.7867 (ptpp) cc_final: 0.7297 (ptpp) REVERT: D 200 GLN cc_start: 0.8277 (pp30) cc_final: 0.7692 (pp30) REVERT: D 202 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8346 (mtm-85) REVERT: D 203 GLU cc_start: 0.8564 (pp20) cc_final: 0.8232 (pp20) REVERT: D 211 GLU cc_start: 0.8052 (pp20) cc_final: 0.7566 (pp20) REVERT: D 215 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8192 (mmtt) REVERT: D 216 LYS cc_start: 0.8678 (tppt) cc_final: 0.8368 (mmmm) REVERT: D 219 LYS cc_start: 0.8471 (mttt) cc_final: 0.8036 (mttt) REVERT: D 222 LYS cc_start: 0.8407 (mptt) cc_final: 0.7960 (mptt) REVERT: D 233 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7956 (mmmm) REVERT: D 236 TRP cc_start: 0.8860 (m-10) cc_final: 0.8580 (m-10) REVERT: D 278 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7904 (ttm110) REVERT: D 295 GLU cc_start: 0.7951 (tt0) cc_final: 0.7501 (tt0) REVERT: D 301 GLU cc_start: 0.7890 (tp30) cc_final: 0.7570 (tm-30) REVERT: D 378 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7715 (mmmm) REVERT: D 398 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8149 (mmmt) REVERT: D 400 MET cc_start: 0.8585 (mtm) cc_final: 0.7886 (mtm) REVERT: D 416 ILE cc_start: 0.8025 (mm) cc_final: 0.7787 (tp) REVERT: D 432 LEU cc_start: 0.8387 (mm) cc_final: 0.8004 (mm) REVERT: D 466 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7395 (mmp) REVERT: D 479 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7404 (tm-30) REVERT: D 506 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7924 (p) REVERT: D 511 TYR cc_start: 0.7569 (t80) cc_final: 0.6954 (t80) REVERT: D 513 MET cc_start: 0.7850 (tpt) cc_final: 0.7596 (tpp) REVERT: D 525 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6720 (ptp) REVERT: D 531 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8007 (ttmm) REVERT: D 556 GLU cc_start: 0.6574 (tp30) cc_final: 0.6274 (tp30) REVERT: D 566 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7657 (mtpp) REVERT: D 568 SER cc_start: 0.7501 (m) cc_final: 0.7054 (t) REVERT: D 571 ASP cc_start: 0.7582 (p0) cc_final: 0.7303 (p0) REVERT: D 622 ASP cc_start: 0.7849 (m-30) cc_final: 0.7608 (m-30) REVERT: D 644 MET cc_start: 0.7931 (mpp) cc_final: 0.7649 (mtm) REVERT: D 678 ARG cc_start: 0.8639 (ppt170) cc_final: 0.7813 (ttp80) REVERT: D 681 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7859 (ttpp) REVERT: D 698 MET cc_start: 0.7684 (tpt) cc_final: 0.6782 (tmm) REVERT: D 702 GLN cc_start: 0.8040 (pt0) cc_final: 0.7588 (pp30) REVERT: D 715 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7974 (ttmm) REVERT: D 728 SER cc_start: 0.7992 (p) cc_final: 0.7591 (m) REVERT: D 781 LYS cc_start: 0.8637 (tptp) cc_final: 0.8208 (tppt) REVERT: D 805 GLN cc_start: 0.7945 (pm20) cc_final: 0.7599 (pm20) REVERT: D 806 ASP cc_start: 0.7482 (p0) cc_final: 0.6616 (t0) REVERT: D 808 VAL cc_start: 0.8446 (t) cc_final: 0.8106 (p) REVERT: D 811 GLU cc_start: 0.7659 (tp30) cc_final: 0.7349 (tp30) REVERT: D 838 ARG cc_start: 0.7803 (tpt-90) cc_final: 0.7490 (mmm-85) REVERT: D 867 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7428 (tm-30) REVERT: D 877 VAL cc_start: 0.8262 (t) cc_final: 0.7970 (p) REVERT: D 881 LYS cc_start: 0.7919 (tppt) cc_final: 0.7660 (tppt) REVERT: D 913 GLU cc_start: 0.7889 (tp30) cc_final: 0.7556 (tp30) REVERT: D 964 LYS cc_start: 0.7967 (tppt) cc_final: 0.7736 (tppt) REVERT: D 992 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7713 (mmtt) REVERT: D 993 GLU cc_start: 0.6288 (mm-30) cc_final: 0.5915 (mm-30) REVERT: D 1007 ASP cc_start: 0.8118 (t70) cc_final: 0.7879 (t0) REVERT: D 1040 MET cc_start: 0.6552 (tpp) cc_final: 0.4242 (mmm) REVERT: D 1095 MET cc_start: 0.6543 (pmm) cc_final: 0.6227 (pmm) REVERT: D 1101 LEU cc_start: 0.8640 (tp) cc_final: 0.7951 (pp) REVERT: D 1119 ASP cc_start: 0.7920 (t0) cc_final: 0.7601 (m-30) REVERT: D 1146 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8025 (mm-30) REVERT: D 1189 MET cc_start: 0.7193 (mmp) cc_final: 0.6711 (mmp) REVERT: D 1203 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6936 (tpt90) REVERT: D 1231 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6944 (ttm-80) REVERT: D 1244 GLN cc_start: 0.8282 (tt0) cc_final: 0.7602 (tm-30) REVERT: D 1247 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7283 (ttmt) REVERT: D 1291 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8200 (mm-30) REVERT: D 1334 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 1352 ILE cc_start: 0.8330 (tp) cc_final: 0.7922 (tt) REVERT: E 53 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6995 (mm-30) REVERT: E 59 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7484 (mp) REVERT: E 68 GLU cc_start: 0.8213 (tp30) cc_final: 0.7819 (tp30) outliers start: 84 outliers final: 61 residues processed: 791 average time/residue: 0.4499 time to fit residues: 525.0536 Evaluate side-chains 820 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 744 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 70 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 232 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107257 restraints weight = 48574.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110946 restraints weight = 25656.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113426 restraints weight = 16187.190| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26848 Z= 0.245 Angle : 0.732 13.685 36556 Z= 0.368 Chirality : 0.044 0.209 4184 Planarity : 0.005 0.076 4544 Dihedral : 14.583 174.278 4287 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.32 % Allowed : 24.78 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.88 (0.15), residues: 3164 helix: 0.53 (0.16), residues: 1079 sheet: -0.17 (0.27), residues: 350 loop : -1.43 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP D 33 HIS 0.009 0.001 HIS C1023 PHE 0.032 0.001 PHE C 514 TYR 0.026 0.002 TYR D 165 ARG 0.013 0.001 ARG D 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8279.67 seconds wall clock time: 148 minutes 51.85 seconds (8931.85 seconds total)