Starting phenix.real_space_refine on Tue Mar 19 09:42:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjg_10217/03_2024/6sjg_10217.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjg_10217/03_2024/6sjg_10217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjg_10217/03_2024/6sjg_10217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjg_10217/03_2024/6sjg_10217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjg_10217/03_2024/6sjg_10217.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjg_10217/03_2024/6sjg_10217.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 101 5.16 5 C 14897 2.51 5 N 4192 2.21 5 O 4582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 728": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1015": "NH1" <-> "NH2" Residue "B ARG 1106": "NH1" <-> "NH2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 877": "NH1" <-> "NH2" Residue "C TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1007": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23826 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4603 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 25, 'TRANS': 571} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1098 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Time building chain proxies: 13.25, per 1000 atoms: 0.56 Number of scatterers: 23826 At special positions: 0 Unit cell: (150.912, 149.864, 129.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 54 15.00 O 4582 8.00 N 4192 7.00 C 14897 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: 9.16 Conformation dependent library (CDL) restraints added in 4.4 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 16 sheets defined 53.5% alpha, 9.2% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 7.24 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.516A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.527A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.780A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.810A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.797A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.326A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.661A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.572A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.734A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.724A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.522A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.550A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.770A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.737A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 removed outlier: 3.556A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 removed outlier: 3.532A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.595A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.927A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.882A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.759A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.574A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.530A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.969A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.599A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.820A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.971A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 962 Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 1000 removed outlier: 3.724A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.755A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.698A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.888A pdb=" N ALA B1048 " --> pdb=" O PRO B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.638A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.041A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.730A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.789A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix removed outlier: 3.509A pdb=" N LYS C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.798A pdb=" N LEU C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.510A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.553A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.758A pdb=" N LEU C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 282 through 287' Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.546A pdb=" N TYR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.516A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.561A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 removed outlier: 3.744A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 459 removed outlier: 4.040A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 removed outlier: 3.502A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.702A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.884A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.657A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.363A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.732A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.541A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 874 through 889 Processing helix chain 'C' and resid 893 through 904 removed outlier: 3.672A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.872A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 935 No H-bonds generated for 'chain 'C' and resid 933 through 935' Processing helix chain 'C' and resid 973 through 989 removed outlier: 3.565A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.911A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.602A pdb=" N GLU C1076 " --> pdb=" O LEU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.800A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.716A pdb=" N GLN D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 15' Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.922A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.508A pdb=" N VAL D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 221 removed outlier: 3.591A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.515A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 244' Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.655A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.536A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.822A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.552A pdb=" N ALA D 319 " --> pdb=" O TYR D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.543A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 365 through 375 removed outlier: 3.977A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.595A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.884A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.553A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.522A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.762A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.428A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 60 " --> pdb=" O MET B 382 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP B 384 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.230A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.517A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.718A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1017 through 1027 removed outlier: 6.688A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.215A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.001A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.661A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 442 through 443 removed outlier: 4.060A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 650 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.602A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.508A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.186A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 5.993A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 6.886A pdb=" N SER D 167 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLY D 296 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE D 169 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.248A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.419A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 9.01 Time building geometry restraints manager: 10.01 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: 6697 1.34 - 1.45: 4289 1.45 - 1.57: 13191 1.57 - 1.69: 106 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" N GLU B1073 " pdb=" CA GLU B1073 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.86e+00 bond pdb=" N PRO B1051 " pdb=" CA PRO B1051 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.31e-02 5.83e+03 2.85e+00 bond pdb=" CA THR B 304 " pdb=" C THR B 304 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.51e+00 bond pdb=" C MET B 658 " pdb=" N PRO B 659 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 1.99e+00 bond pdb=" CA TYR B 173 " pdb=" C TYR B 173 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.14e-02 7.69e+03 1.98e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.51: 1065 106.51 - 113.41: 12955 113.41 - 120.30: 9436 120.30 - 127.19: 9579 127.19 - 134.09: 374 Bond angle restraints: 33409 Sorted by residual: angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C VAL B 657 " pdb=" N MET B 658 " pdb=" CA MET B 658 " ideal model delta sigma weight residual 120.09 124.51 -4.42 1.25e+00 6.40e-01 1.25e+01 angle pdb=" C ASN B1084 " pdb=" N TRP B1085 " pdb=" CA TRP B1085 " ideal model delta sigma weight residual 122.82 127.75 -4.93 1.42e+00 4.96e-01 1.20e+01 angle pdb=" N GLY B 656 " pdb=" CA GLY B 656 " pdb=" C GLY B 656 " ideal model delta sigma weight residual 110.60 115.08 -4.48 1.46e+00 4.69e-01 9.44e+00 angle pdb=" C GLN D 387 " pdb=" N GLN D 388 " pdb=" CA GLN D 388 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.40e+00 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 13492 16.78 - 33.57: 730 33.57 - 50.35: 307 50.35 - 67.14: 79 67.14 - 83.92: 7 Dihedral angle restraints: 14615 sinusoidal: 6326 harmonic: 8289 Sorted by residual: dihedral pdb=" CA ILE B 400 " pdb=" C ILE B 400 " pdb=" N TRP B 401 " pdb=" CA TRP B 401 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N ASN C 768 " pdb=" CA ASN C 768 " pdb=" CB ASN C 768 " pdb=" CG ASN C 768 " ideal model delta sinusoidal sigma weight residual -60.00 -118.97 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2613 0.034 - 0.069: 745 0.069 - 0.103: 227 0.103 - 0.137: 78 0.137 - 0.171: 10 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA LEU C 588 " pdb=" N LEU C 588 " pdb=" C LEU C 588 " pdb=" CB LEU C 588 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA TYR B 173 " pdb=" N TYR B 173 " pdb=" C TYR B 173 " pdb=" CB TYR B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU C 99 " pdb=" N LEU C 99 " pdb=" C LEU C 99 " pdb=" CB LEU C 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO C 658 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 420 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 99 " 0.036 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO C 100 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " 0.030 5.00e-02 4.00e+02 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6709 2.82 - 3.34: 19747 3.34 - 3.86: 39494 3.86 - 4.38: 44353 4.38 - 4.90: 76387 Nonbonded interactions: 186690 Sorted by model distance: nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.294 2.440 nonbonded pdb=" O THR D 533 " pdb=" OG1 THR D 533 " model vdw 2.321 2.440 nonbonded pdb=" OH TYR C 794 " pdb=" O ALA C 803 " model vdw 2.332 2.440 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.333 2.440 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.334 2.496 ... (remaining 186685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.080 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: 4.350 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 68.570 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 0.045 24452 Z= 0.163 Angle : 0.558 8.094 33409 Z= 0.336 Chirality : 0.039 0.171 3673 Planarity : 0.005 0.075 4205 Dihedral : 12.823 83.921 9243 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.90 % Allowed : 4.89 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -3.61 (0.11), residues: 2837 helix: -2.53 (0.09), residues: 1384 sheet: -0.89 (0.27), residues: 284 loop : -2.43 (0.14), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 652 HIS 0.004 0.000 HIS D 256 PHE 0.014 0.001 PHE B1023 TYR 0.012 0.001 TYR B1111 ARG 0.004 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 577 time to evaluate : 2.375 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: B 66 GLU cc_start: 0.7112 (tt0) cc_final: 0.6737 (tp30) REVERT: B 137 LEU cc_start: 0.9029 (mt) cc_final: 0.8822 (mt) REVERT: B 304 THR cc_start: 0.2275 (OUTLIER) cc_final: 0.1073 (p) REVERT: B 354 MET cc_start: 0.8311 (mtt) cc_final: 0.7980 (mtm) REVERT: B 514 TYR cc_start: 0.5926 (t80) cc_final: 0.5725 (t80) REVERT: B 735 LEU cc_start: 0.5925 (mt) cc_final: 0.5497 (mp) REVERT: B 756 PHE cc_start: 0.7654 (m-80) cc_final: 0.7350 (m-80) REVERT: B 842 LEU cc_start: 0.8491 (mt) cc_final: 0.8277 (mt) REVERT: B 860 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7913 (pt) REVERT: B 940 LEU cc_start: 0.6118 (mt) cc_final: 0.5759 (mm) REVERT: B 1024 TYR cc_start: 0.5652 (m-80) cc_final: 0.5400 (m-10) REVERT: B 1058 VAL cc_start: 0.7867 (t) cc_final: 0.7390 (m) REVERT: B 1158 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.6518 (p) REVERT: C 460 LEU cc_start: 0.8937 (tp) cc_final: 0.8648 (tt) REVERT: C 697 MET cc_start: 0.7577 (mtp) cc_final: 0.6978 (mtp) REVERT: C 781 THR cc_start: 0.8165 (m) cc_final: 0.7800 (p) REVERT: C 817 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7159 (m90) REVERT: C 1000 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8549 (mt) REVERT: D 216 LEU cc_start: 0.5196 (mt) cc_final: 0.4768 (pp) REVERT: D 407 MET cc_start: 0.6652 (ttp) cc_final: 0.5882 (ptm) REVERT: D 415 TYR cc_start: 0.2918 (m-80) cc_final: 0.2246 (m-80) REVERT: D 430 LEU cc_start: 0.8443 (mp) cc_final: 0.8061 (mp) REVERT: D 462 MET cc_start: 0.4050 (mmt) cc_final: 0.3782 (mmt) REVERT: D 493 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7712 (pp) REVERT: D 558 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.6360 (t) REVERT: D 567 TYR cc_start: 0.7747 (t80) cc_final: 0.7459 (t80) REVERT: D 571 THR cc_start: 0.7677 (p) cc_final: 0.7474 (p) outliers start: 70 outliers final: 9 residues processed: 631 average time/residue: 0.3861 time to fit residues: 364.9965 Evaluate side-chains 310 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 294 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 558 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN B 134 GLN B 181 GLN B 458 ASN B 525 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 713 GLN B 765 GLN B 843 GLN B 848 GLN B 944 GLN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS B1084 ASN B1133 HIS B1134 HIS C 113 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 191 GLN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS C 423 GLN C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 725 GLN C 749 GLN C 759 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN C 979 GLN C 984 HIS C1091 GLN C1108 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 79 GLN D 89 GLN D 115 ASN D 128 HIS D 251 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.151 24452 Z= 0.434 Angle : 0.757 12.955 33409 Z= 0.383 Chirality : 0.044 0.239 3673 Planarity : 0.006 0.057 4205 Dihedral : 13.484 80.662 3729 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.89 % Allowed : 12.55 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -1.42 (0.14), residues: 2837 helix: -0.22 (0.13), residues: 1426 sheet: -0.59 (0.29), residues: 297 loop : -1.92 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C1045 HIS 0.009 0.002 HIS C 233 PHE 0.020 0.002 PHE C 86 TYR 0.019 0.002 TYR C 535 ARG 0.007 0.001 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 273 time to evaluate : 2.675 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: B 321 LEU cc_start: 0.8353 (mt) cc_final: 0.8096 (mp) REVERT: B 354 MET cc_start: 0.8440 (mtt) cc_final: 0.8099 (mtm) REVERT: B 492 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7141 (pptt) REVERT: B 660 MET cc_start: 0.7641 (tmm) cc_final: 0.7439 (tmm) REVERT: B 753 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8478 (t60) REVERT: B 871 GLN cc_start: 0.5827 (tt0) cc_final: 0.5079 (mp10) REVERT: B 1002 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7542 (pp) REVERT: B 1004 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8014 (pm20) REVERT: B 1066 ILE cc_start: 0.8495 (mt) cc_final: 0.8238 (mm) REVERT: C 1 MET cc_start: 0.5626 (tpt) cc_final: 0.5375 (tmm) REVERT: C 569 MET cc_start: 0.6879 (tmm) cc_final: 0.6616 (tmm) REVERT: C 653 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7167 (mpp80) REVERT: C 680 MET cc_start: 0.8819 (mmp) cc_final: 0.8557 (mmp) REVERT: C 781 THR cc_start: 0.8887 (m) cc_final: 0.8662 (p) REVERT: C 817 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7208 (m90) REVERT: C 1000 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9052 (mt) REVERT: D 112 MET cc_start: 0.7871 (mmm) cc_final: 0.7490 (ttm) REVERT: D 125 GLU cc_start: 0.8605 (pt0) cc_final: 0.8320 (pp20) REVERT: D 269 ASP cc_start: 0.8293 (p0) cc_final: 0.8048 (p0) REVERT: D 270 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8011 (tp30) REVERT: D 415 TYR cc_start: 0.3093 (m-80) cc_final: 0.2691 (m-80) REVERT: D 433 GLN cc_start: 0.7716 (mt0) cc_final: 0.7386 (mp10) REVERT: D 462 MET cc_start: 0.4456 (mmt) cc_final: 0.4140 (mmt) REVERT: D 567 TYR cc_start: 0.7902 (t80) cc_final: 0.7532 (t80) REVERT: D 575 ARG cc_start: 0.7379 (tpp80) cc_final: 0.7094 (tpt90) outliers start: 94 outliers final: 48 residues processed: 351 average time/residue: 0.3563 time to fit residues: 193.9799 Evaluate side-chains 263 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 562 GLN Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 262 optimal weight: 0.0070 chunk 283 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 210 optimal weight: 0.9980 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN B 868 GLN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN D 318 ASN D 423 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24452 Z= 0.192 Angle : 0.563 9.754 33409 Z= 0.283 Chirality : 0.039 0.165 3673 Planarity : 0.004 0.053 4205 Dihedral : 13.373 84.204 3720 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.86 % Allowed : 14.16 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.49 (0.15), residues: 2837 helix: 0.70 (0.13), residues: 1420 sheet: -0.38 (0.30), residues: 287 loop : -1.63 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 574 HIS 0.007 0.001 HIS B 222 PHE 0.016 0.001 PHE B 351 TYR 0.015 0.001 TYR C 535 ARG 0.011 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 240 time to evaluate : 2.769 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: B 354 MET cc_start: 0.8374 (mtt) cc_final: 0.7920 (mtm) REVERT: B 492 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7279 (pptt) REVERT: B 499 MET cc_start: 0.7768 (tmm) cc_final: 0.7292 (tmm) REVERT: B 753 TRP cc_start: 0.8961 (OUTLIER) cc_final: 0.8143 (t60) REVERT: B 871 GLN cc_start: 0.5780 (tt0) cc_final: 0.5192 (mp10) REVERT: B 1002 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7609 (pp) REVERT: B 1004 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8038 (pm20) REVERT: B 1098 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5610 (mpp) REVERT: B 1140 TYR cc_start: 0.7358 (m-80) cc_final: 0.6690 (m-80) REVERT: C 653 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7548 (mpp80) REVERT: C 665 MET cc_start: 0.7349 (mmm) cc_final: 0.7110 (tpt) REVERT: C 781 THR cc_start: 0.8948 (m) cc_final: 0.8649 (p) REVERT: D 112 MET cc_start: 0.7689 (mmm) cc_final: 0.7388 (ttm) REVERT: D 125 GLU cc_start: 0.8646 (pt0) cc_final: 0.8356 (pp20) REVERT: D 222 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: D 269 ASP cc_start: 0.8031 (p0) cc_final: 0.7586 (p0) REVERT: D 270 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7856 (tp30) REVERT: D 415 TYR cc_start: 0.3222 (m-80) cc_final: 0.2633 (m-80) REVERT: D 429 ASP cc_start: 0.5669 (m-30) cc_final: 0.5217 (m-30) REVERT: D 433 GLN cc_start: 0.7673 (mt0) cc_final: 0.7301 (mp10) REVERT: D 462 MET cc_start: 0.4367 (mmt) cc_final: 0.3989 (mmt) REVERT: D 484 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6319 (tp) REVERT: D 504 ARG cc_start: 0.8579 (ptm160) cc_final: 0.8135 (ptp90) outliers start: 69 outliers final: 39 residues processed: 298 average time/residue: 0.3391 time to fit residues: 160.1144 Evaluate side-chains 254 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 209 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 551 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 262 optimal weight: 30.0000 chunk 278 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24452 Z= 0.287 Angle : 0.615 8.271 33409 Z= 0.307 Chirality : 0.041 0.212 3673 Planarity : 0.004 0.065 4205 Dihedral : 13.465 83.293 3714 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.19 % Allowed : 14.62 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2837 helix: 1.09 (0.14), residues: 1424 sheet: -0.47 (0.29), residues: 295 loop : -1.56 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 574 HIS 0.007 0.001 HIS B 222 PHE 0.018 0.002 PHE B 351 TYR 0.014 0.002 TYR C 535 ARG 0.006 0.001 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 214 time to evaluate : 2.382 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: B 146 MET cc_start: 0.7788 (ttt) cc_final: 0.7549 (ttt) REVERT: B 286 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7100 (mm) REVERT: B 354 MET cc_start: 0.8311 (mtt) cc_final: 0.7862 (mtm) REVERT: B 492 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7509 (pptt) REVERT: B 499 MET cc_start: 0.7959 (tmm) cc_final: 0.7565 (tmm) REVERT: B 753 TRP cc_start: 0.9079 (OUTLIER) cc_final: 0.8482 (t60) REVERT: B 871 GLN cc_start: 0.5853 (tt0) cc_final: 0.5389 (mp10) REVERT: B 993 TRP cc_start: 0.7811 (t60) cc_final: 0.7224 (t60) REVERT: B 1098 MET cc_start: 0.5965 (mpp) cc_final: 0.5647 (mpp) REVERT: B 1102 MET cc_start: 0.7512 (mmm) cc_final: 0.7245 (tpt) REVERT: B 1140 TYR cc_start: 0.7576 (m-80) cc_final: 0.5713 (m-80) REVERT: C 531 MET cc_start: 0.8143 (mpp) cc_final: 0.7663 (mpp) REVERT: C 569 MET cc_start: 0.6425 (tmm) cc_final: 0.6135 (tmm) REVERT: C 781 THR cc_start: 0.9152 (m) cc_final: 0.8873 (p) REVERT: D 112 MET cc_start: 0.7850 (mmm) cc_final: 0.7550 (ttm) REVERT: D 222 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: D 269 ASP cc_start: 0.8034 (p0) cc_final: 0.7695 (p0) REVERT: D 270 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7593 (tp30) REVERT: D 415 TYR cc_start: 0.3510 (m-80) cc_final: 0.2842 (m-80) REVERT: D 462 MET cc_start: 0.4408 (mmt) cc_final: 0.4197 (mmt) REVERT: D 466 ARG cc_start: 0.6666 (mmt-90) cc_final: 0.6442 (tpp-160) REVERT: D 484 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6183 (tp) REVERT: D 514 MET cc_start: 0.6305 (mmt) cc_final: 0.5214 (mtt) REVERT: D 575 ARG cc_start: 0.7677 (tpt90) cc_final: 0.7460 (tpt-90) outliers start: 77 outliers final: 50 residues processed: 274 average time/residue: 0.3254 time to fit residues: 144.8970 Evaluate side-chains 255 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24452 Z= 0.155 Angle : 0.540 11.233 33409 Z= 0.267 Chirality : 0.038 0.172 3673 Planarity : 0.004 0.056 4205 Dihedral : 13.420 84.251 3712 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.69 % Allowed : 15.28 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.22 (0.16), residues: 2837 helix: 1.42 (0.14), residues: 1423 sheet: -0.38 (0.30), residues: 280 loop : -1.38 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 153 HIS 0.004 0.001 HIS B 222 PHE 0.012 0.001 PHE B 64 TYR 0.018 0.001 TYR B1111 ARG 0.005 0.000 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 211 time to evaluate : 2.498 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: B 354 MET cc_start: 0.8240 (mtt) cc_final: 0.7803 (mtm) REVERT: B 492 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7644 (pptt) REVERT: B 753 TRP cc_start: 0.9044 (OUTLIER) cc_final: 0.8397 (t60) REVERT: B 871 GLN cc_start: 0.5774 (tt0) cc_final: 0.5373 (mp10) REVERT: B 1002 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 1098 MET cc_start: 0.6007 (mpp) cc_final: 0.5752 (mpp) REVERT: B 1111 TYR cc_start: 0.6861 (t80) cc_final: 0.6514 (t80) REVERT: B 1140 TYR cc_start: 0.7421 (m-80) cc_final: 0.6478 (m-80) REVERT: B 1168 MET cc_start: 0.7140 (mtm) cc_final: 0.6823 (mtm) REVERT: C 411 MET cc_start: 0.8137 (mmt) cc_final: 0.7718 (mmt) REVERT: C 653 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7452 (mpp80) REVERT: C 667 MET cc_start: 0.6095 (mmt) cc_final: 0.5633 (mmm) REVERT: C 781 THR cc_start: 0.9043 (m) cc_final: 0.8805 (p) REVERT: D 95 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6187 (p0) REVERT: D 112 MET cc_start: 0.7865 (mmm) cc_final: 0.7500 (ttm) REVERT: D 222 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: D 269 ASP cc_start: 0.7939 (p0) cc_final: 0.7558 (p0) REVERT: D 270 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7756 (tp30) REVERT: D 275 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6610 (p0) REVERT: D 415 TYR cc_start: 0.3306 (m-80) cc_final: 0.2686 (m-80) REVERT: D 417 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.7289 (ptt-90) REVERT: D 462 MET cc_start: 0.4356 (mmt) cc_final: 0.4012 (mmt) REVERT: D 484 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6137 (tp) REVERT: D 514 MET cc_start: 0.6431 (mmt) cc_final: 0.5550 (mtt) REVERT: D 575 ARG cc_start: 0.7546 (tpt90) cc_final: 0.7304 (tpt-90) outliers start: 65 outliers final: 41 residues processed: 265 average time/residue: 0.3132 time to fit residues: 135.1367 Evaluate side-chains 248 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 278 optimal weight: 30.0000 chunk 231 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24452 Z= 0.276 Angle : 0.605 9.628 33409 Z= 0.300 Chirality : 0.040 0.182 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.566 85.108 3710 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.11 % Allowed : 15.40 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.25 (0.16), residues: 2837 helix: 1.45 (0.14), residues: 1419 sheet: -0.55 (0.29), residues: 306 loop : -1.33 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 153 HIS 0.007 0.001 HIS B 222 PHE 0.029 0.002 PHE B 289 TYR 0.012 0.002 TYR B 37 ARG 0.008 0.001 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 209 time to evaluate : 2.521 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: B 354 MET cc_start: 0.8318 (mtt) cc_final: 0.7829 (mtm) REVERT: B 492 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7941 (pptt) REVERT: B 753 TRP cc_start: 0.9118 (OUTLIER) cc_final: 0.8541 (t60) REVERT: B 871 GLN cc_start: 0.6211 (tt0) cc_final: 0.5701 (mp10) REVERT: B 1098 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5613 (mpp) REVERT: B 1111 TYR cc_start: 0.6985 (t80) cc_final: 0.6546 (t80) REVERT: B 1140 TYR cc_start: 0.7517 (m-80) cc_final: 0.6165 (m-10) REVERT: B 1168 MET cc_start: 0.7259 (mtm) cc_final: 0.6915 (mtm) REVERT: C 1 MET cc_start: 0.6031 (tpt) cc_final: 0.5632 (tmm) REVERT: C 411 MET cc_start: 0.8187 (mmt) cc_final: 0.7687 (mmt) REVERT: C 653 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7630 (mpp80) REVERT: C 667 MET cc_start: 0.6355 (mmt) cc_final: 0.5983 (mmm) REVERT: C 781 THR cc_start: 0.9205 (m) cc_final: 0.8980 (p) REVERT: C 787 MET cc_start: 0.8694 (mmp) cc_final: 0.8376 (mmm) REVERT: C 1000 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9219 (mt) REVERT: D 95 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6479 (p0) REVERT: D 125 GLU cc_start: 0.8638 (pt0) cc_final: 0.8290 (pp20) REVERT: D 222 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: D 269 ASP cc_start: 0.8006 (p0) cc_final: 0.7727 (p0) REVERT: D 270 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7577 (tp30) REVERT: D 275 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6673 (p0) REVERT: D 415 TYR cc_start: 0.3823 (m-80) cc_final: 0.3115 (m-80) REVERT: D 462 MET cc_start: 0.4472 (mmt) cc_final: 0.4208 (mmt) REVERT: D 466 ARG cc_start: 0.6698 (mmt-90) cc_final: 0.6396 (tpp-160) REVERT: D 484 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6210 (tp) REVERT: D 514 MET cc_start: 0.6452 (mmt) cc_final: 0.5545 (mtt) REVERT: D 575 ARG cc_start: 0.7553 (tpt90) cc_final: 0.7323 (tpt-90) outliers start: 75 outliers final: 49 residues processed: 273 average time/residue: 0.3541 time to fit residues: 156.9073 Evaluate side-chains 255 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 198 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 203 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 277 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24452 Z= 0.210 Angle : 0.569 9.477 33409 Z= 0.280 Chirality : 0.040 0.195 3673 Planarity : 0.004 0.053 4205 Dihedral : 13.601 89.592 3710 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.44 % Allowed : 15.86 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2837 helix: 1.52 (0.14), residues: 1427 sheet: -0.50 (0.30), residues: 295 loop : -1.26 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 153 HIS 0.005 0.001 HIS B 222 PHE 0.018 0.001 PHE B 428 TYR 0.014 0.001 TYR B1111 ARG 0.006 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 211 time to evaluate : 2.607 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: B 354 MET cc_start: 0.8225 (mtt) cc_final: 0.7766 (mtm) REVERT: B 492 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8139 (pptt) REVERT: B 735 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4432 (mp) REVERT: B 753 TRP cc_start: 0.9123 (OUTLIER) cc_final: 0.8575 (t60) REVERT: B 993 TRP cc_start: 0.7778 (t60) cc_final: 0.7218 (t60) REVERT: B 1098 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5509 (mpp) REVERT: B 1111 TYR cc_start: 0.7044 (t80) cc_final: 0.6632 (t80) REVERT: B 1140 TYR cc_start: 0.7683 (m-80) cc_final: 0.6490 (m-80) REVERT: C 411 MET cc_start: 0.8375 (mmt) cc_final: 0.7625 (mmt) REVERT: C 572 ASN cc_start: 0.8476 (t0) cc_final: 0.8126 (t0) REVERT: C 667 MET cc_start: 0.6265 (mmt) cc_final: 0.5860 (mmm) REVERT: C 781 THR cc_start: 0.9242 (m) cc_final: 0.9011 (p) REVERT: C 1000 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9170 (mt) REVERT: D 95 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6512 (p0) REVERT: D 112 MET cc_start: 0.7825 (mtm) cc_final: 0.7586 (ttm) REVERT: D 125 GLU cc_start: 0.8679 (pt0) cc_final: 0.8314 (pp20) REVERT: D 222 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: D 269 ASP cc_start: 0.8098 (p0) cc_final: 0.7784 (p0) REVERT: D 270 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7573 (tp30) REVERT: D 275 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6624 (p0) REVERT: D 415 TYR cc_start: 0.3689 (m-80) cc_final: 0.2962 (m-80) REVERT: D 466 ARG cc_start: 0.6719 (mmt-90) cc_final: 0.6334 (tpp-160) REVERT: D 484 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6214 (tp) REVERT: D 511 TRP cc_start: 0.7954 (m100) cc_final: 0.7244 (m100) REVERT: D 514 MET cc_start: 0.6434 (mmt) cc_final: 0.5507 (mtt) REVERT: D 575 ARG cc_start: 0.7529 (tpt90) cc_final: 0.7291 (tpt-90) outliers start: 83 outliers final: 57 residues processed: 274 average time/residue: 0.3227 time to fit residues: 143.0895 Evaluate side-chains 270 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 204 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 582 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 137 optimal weight: 0.0370 chunk 25 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24452 Z= 0.168 Angle : 0.563 13.512 33409 Z= 0.274 Chirality : 0.039 0.208 3673 Planarity : 0.003 0.056 4205 Dihedral : 13.568 87.829 3710 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.90 % Allowed : 16.36 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.49 (0.16), residues: 2837 helix: 1.62 (0.14), residues: 1429 sheet: -0.37 (0.30), residues: 293 loop : -1.21 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 153 HIS 0.005 0.001 HIS D 241 PHE 0.013 0.001 PHE B 132 TYR 0.017 0.001 TYR C 685 ARG 0.006 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 214 time to evaluate : 2.487 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: B 354 MET cc_start: 0.8190 (mtt) cc_final: 0.7791 (mtm) REVERT: B 492 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8297 (pptt) REVERT: B 735 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4541 (mp) REVERT: B 753 TRP cc_start: 0.9030 (OUTLIER) cc_final: 0.8503 (t60) REVERT: B 993 TRP cc_start: 0.7729 (t60) cc_final: 0.7188 (t60) REVERT: B 1098 MET cc_start: 0.5921 (mpp) cc_final: 0.5576 (mpp) REVERT: B 1111 TYR cc_start: 0.7001 (t80) cc_final: 0.6489 (t80) REVERT: B 1140 TYR cc_start: 0.7700 (m-80) cc_final: 0.6220 (m-80) REVERT: B 1156 TYR cc_start: 0.8109 (t80) cc_final: 0.7732 (t80) REVERT: C 411 MET cc_start: 0.8448 (mmt) cc_final: 0.8128 (mtp) REVERT: C 490 LEU cc_start: 0.8316 (tt) cc_final: 0.8073 (tp) REVERT: C 572 ASN cc_start: 0.8462 (t0) cc_final: 0.8029 (t0) REVERT: C 667 MET cc_start: 0.6166 (mmt) cc_final: 0.5782 (mmm) REVERT: C 781 THR cc_start: 0.9203 (m) cc_final: 0.8974 (p) REVERT: C 965 LEU cc_start: 0.8564 (tp) cc_final: 0.8347 (tp) REVERT: C 1000 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9142 (mt) REVERT: D 95 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6576 (p0) REVERT: D 112 MET cc_start: 0.7836 (mtm) cc_final: 0.7533 (ttm) REVERT: D 125 GLU cc_start: 0.8673 (pt0) cc_final: 0.8330 (pp20) REVERT: D 222 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: D 269 ASP cc_start: 0.8067 (p0) cc_final: 0.7767 (p0) REVERT: D 270 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7720 (tp30) REVERT: D 275 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6640 (p0) REVERT: D 415 TYR cc_start: 0.3793 (m-80) cc_final: 0.3062 (m-80) REVERT: D 511 TRP cc_start: 0.8012 (m100) cc_final: 0.7287 (m100) REVERT: D 514 MET cc_start: 0.6376 (mmt) cc_final: 0.5534 (mtt) REVERT: D 575 ARG cc_start: 0.7538 (tpt90) cc_final: 0.7336 (tpt-90) outliers start: 70 outliers final: 50 residues processed: 270 average time/residue: 0.3208 time to fit residues: 141.9577 Evaluate side-chains 257 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 200 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 8.9990 chunk 265 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 258 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24452 Z= 0.199 Angle : 0.591 12.560 33409 Z= 0.287 Chirality : 0.040 0.336 3673 Planarity : 0.004 0.054 4205 Dihedral : 13.577 87.017 3710 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.77 % Allowed : 17.10 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.51 (0.16), residues: 2837 helix: 1.63 (0.14), residues: 1430 sheet: -0.30 (0.30), residues: 295 loop : -1.21 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 153 HIS 0.005 0.001 HIS D 241 PHE 0.014 0.001 PHE B 428 TYR 0.018 0.001 TYR B1111 ARG 0.007 0.000 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 206 time to evaluate : 2.806 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: B 492 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8351 (pptt) REVERT: B 735 LEU cc_start: 0.5354 (OUTLIER) cc_final: 0.4891 (mp) REVERT: B 753 TRP cc_start: 0.9080 (OUTLIER) cc_final: 0.8570 (t60) REVERT: B 993 TRP cc_start: 0.7770 (t60) cc_final: 0.7281 (t60) REVERT: B 1021 MET cc_start: 0.5239 (tpt) cc_final: 0.4901 (tpt) REVERT: B 1098 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5550 (mpp) REVERT: B 1102 MET cc_start: 0.7354 (mmm) cc_final: 0.7064 (tpt) REVERT: B 1111 TYR cc_start: 0.7028 (t80) cc_final: 0.6773 (t80) REVERT: B 1140 TYR cc_start: 0.7843 (m-80) cc_final: 0.6452 (m-80) REVERT: C 411 MET cc_start: 0.8453 (mmt) cc_final: 0.8104 (mtp) REVERT: C 572 ASN cc_start: 0.8468 (t0) cc_final: 0.8056 (t0) REVERT: C 653 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7716 (mpp80) REVERT: C 667 MET cc_start: 0.6150 (mmt) cc_final: 0.5394 (mmm) REVERT: C 781 THR cc_start: 0.9217 (m) cc_final: 0.8997 (p) REVERT: C 1000 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9151 (mt) REVERT: D 95 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.6649 (p0) REVERT: D 112 MET cc_start: 0.7824 (mtm) cc_final: 0.7558 (ttm) REVERT: D 222 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: D 269 ASP cc_start: 0.8162 (p0) cc_final: 0.7815 (p0) REVERT: D 270 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7731 (tp30) REVERT: D 275 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6668 (p0) REVERT: D 415 TYR cc_start: 0.3842 (m-80) cc_final: 0.2787 (m-10) REVERT: D 483 MET cc_start: 0.6771 (ttm) cc_final: 0.6238 (mtp) REVERT: D 514 MET cc_start: 0.6352 (mmt) cc_final: 0.5534 (mtt) outliers start: 67 outliers final: 53 residues processed: 258 average time/residue: 0.3366 time to fit residues: 140.9891 Evaluate side-chains 258 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 197 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 5.9990 chunk 273 optimal weight: 30.0000 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 286 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 24452 Z= 0.340 Angle : 0.695 12.896 33409 Z= 0.343 Chirality : 0.043 0.321 3673 Planarity : 0.005 0.058 4205 Dihedral : 13.788 87.505 3710 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.77 % Allowed : 17.47 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.18 (0.16), residues: 2837 helix: 1.29 (0.14), residues: 1426 sheet: -0.48 (0.30), residues: 298 loop : -1.24 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 153 HIS 0.008 0.001 HIS C 984 PHE 0.014 0.002 PHE C 912 TYR 0.018 0.002 TYR C 685 ARG 0.011 0.001 ARG D 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 201 time to evaluate : 2.691 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: B 492 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8352 (pptt) REVERT: B 735 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5493 (mp) REVERT: B 753 TRP cc_start: 0.9183 (OUTLIER) cc_final: 0.8713 (t60) REVERT: B 1098 MET cc_start: 0.5785 (OUTLIER) cc_final: 0.5309 (mpp) REVERT: B 1111 TYR cc_start: 0.7002 (t80) cc_final: 0.6670 (t80) REVERT: B 1140 TYR cc_start: 0.7813 (m-80) cc_final: 0.6234 (m-80) REVERT: B 1170 GLU cc_start: 0.8677 (pt0) cc_final: 0.8265 (tm-30) REVERT: C 411 MET cc_start: 0.8345 (mmt) cc_final: 0.8023 (mtp) REVERT: C 653 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7261 (ptp90) REVERT: C 667 MET cc_start: 0.6366 (mmt) cc_final: 0.5689 (tpp) REVERT: C 1000 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9253 (mt) REVERT: D 95 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6760 (p0) REVERT: D 112 MET cc_start: 0.7972 (mtm) cc_final: 0.7668 (ttm) REVERT: D 222 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: D 269 ASP cc_start: 0.8179 (p0) cc_final: 0.7805 (p0) REVERT: D 270 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7558 (tp30) REVERT: D 415 TYR cc_start: 0.4241 (m-80) cc_final: 0.3496 (m-80) REVERT: D 466 ARG cc_start: 0.6536 (mmt-90) cc_final: 0.5844 (mmp-170) REVERT: D 483 MET cc_start: 0.6944 (ttm) cc_final: 0.6454 (mtp) REVERT: D 514 MET cc_start: 0.6224 (mmt) cc_final: 0.5346 (mtt) outliers start: 67 outliers final: 53 residues processed: 254 average time/residue: 0.3370 time to fit residues: 138.3299 Evaluate side-chains 249 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 189 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1080 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.0570 chunk 243 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 GLN D 22 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.101795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.076100 restraints weight = 82308.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077521 restraints weight = 50997.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.078598 restraints weight = 38304.729| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 24452 Z= 0.375 Angle : 0.710 12.585 33409 Z= 0.353 Chirality : 0.044 0.331 3673 Planarity : 0.005 0.049 4205 Dihedral : 13.945 88.204 3710 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.94 % Allowed : 17.89 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.02 (0.16), residues: 2837 helix: 1.12 (0.14), residues: 1410 sheet: -0.68 (0.30), residues: 310 loop : -1.26 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 153 HIS 0.007 0.001 HIS C 779 PHE 0.024 0.002 PHE B 428 TYR 0.027 0.002 TYR D 580 ARG 0.007 0.001 ARG C 653 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4236.86 seconds wall clock time: 77 minutes 36.82 seconds (4656.82 seconds total)