Starting phenix.real_space_refine on Tue Mar 19 11:54:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjb_10214/03_2024/6sjb_10214.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjb_10214/03_2024/6sjb_10214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjb_10214/03_2024/6sjb_10214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjb_10214/03_2024/6sjb_10214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjb_10214/03_2024/6sjb_10214.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sjb_10214/03_2024/6sjb_10214.pdb" } resolution = 3.7 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 68 5.49 5 S 101 5.16 5 C 15036 2.51 5 N 4236 2.21 5 O 4674 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 ARG 895": "NH1" <-> "NH2" Residue "B PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 959": "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 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 ARG 186": "NH1" <-> "NH2" 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 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 442": "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 653": "NH1" <-> "NH2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 687": "NH1" <-> "NH2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 396": "NH1" <-> "NH2" 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24115 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: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1387 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain breaks: 1 Time building chain proxies: 12.77, per 1000 atoms: 0.53 Number of scatterers: 24115 At special positions: 0 Unit cell: (151.815, 150.768, 123.546, 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 68 15.00 O 4674 8.00 N 4236 7.00 C 15036 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: 9.05 Conformation dependent library (CDL) restraints added in 4.2 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: 126 helices and 16 sheets defined 53.2% alpha, 9.6% beta 17 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 8.27 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.527A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.691A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.762A 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: 3.538A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.800A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.333A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.707A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.562A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.559A pdb=" N ASN B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.610A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.844A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.349A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.504A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.506A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.816A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.780A 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: 3.511A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 572 removed outlier: 3.552A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.643A 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: 3.944A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.941A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.526A 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 removed outlier: 3.542A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 668 Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.551A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 699 removed outlier: 4.376A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.851A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 745 removed outlier: 3.909A pdb=" N LYS B 745 " --> pdb=" O HIS B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 742 through 745' Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.611A 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 838 through 843 Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.909A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 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: 3.702A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.747A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.858A 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: 3.661A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.937A 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: 3.641A 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 removed outlier: 3.928A pdb=" N HIS C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.691A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.573A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 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 418 through 428 Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.528A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.696A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.850A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.517A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) 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 574 removed outlier: 3.773A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.417A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 644 removed outlier: 4.014A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.803A pdb=" N GLN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 removed outlier: 3.571A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) 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: 3.551A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.711A 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: 3.721A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 4.024A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 989 removed outlier: 3.595A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 4.082A 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: 3.668A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C1069 " --> pdb=" O GLN C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.802A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.565A 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 removed outlier: 3.513A pdb=" N VAL D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.891A 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 removed outlier: 3.576A pdb=" N LEU D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.602A 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 Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.631A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.980A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.540A 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: 3.547A 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: 4.004A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.651A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.890A 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: 3.525A 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 Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.738A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 4.009A 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: 6.410A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.461A 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: 6.352A 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: 6.711A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 5.993A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 901 through 904 removed outlier: 5.993A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.639A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.972A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 7.379A pdb=" N ILE C 408 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N CYS C 662 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL C 410 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 409 " --> pdb=" O CYS C 676 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU C 678 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET C 411 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.507A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.623A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.231A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.286A 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: 6.046A 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: 3.576A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.605A 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: 7.246A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.501A 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: 4.450A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 10.41 Time building geometry restraints manager: 9.84 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: 6774 1.34 - 1.45: 4450 1.45 - 1.57: 13247 1.57 - 1.69: 134 1.69 - 1.81: 169 Bond restraints: 24774 Sorted by residual: bond pdb=" O3' DC X 80 " pdb=" P DT X 81 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.50e-02 4.44e+03 2.33e+01 bond pdb=" P DT X 81 " pdb=" OP1 DT X 81 " ideal model delta sigma weight residual 1.480 1.551 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 1.523 1.561 -0.037 1.30e-02 5.92e+03 8.32e+00 bond pdb=" C4' DT X 81 " pdb=" O4' DT X 81 " ideal model delta sigma weight residual 1.450 1.393 0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" O3' DG X 79 " pdb=" P DC X 80 " ideal model delta sigma weight residual 1.607 1.643 -0.036 1.50e-02 4.44e+03 5.78e+00 ... (remaining 24769 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.37: 1120 106.37 - 113.29: 13091 113.29 - 120.21: 9393 120.21 - 127.12: 9877 127.12 - 134.04: 427 Bond angle restraints: 33908 Sorted by residual: angle pdb=" N LEU C 664 " pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 111.28 122.87 -11.59 1.09e+00 8.42e-01 1.13e+02 angle pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" C MET C 665 " ideal model delta sigma weight residual 113.16 123.90 -10.74 1.42e+00 4.96e-01 5.72e+01 angle pdb=" O3' DG X 79 " pdb=" C3' DG X 79 " pdb=" C2' DG X 79 " ideal model delta sigma weight residual 111.50 120.53 -9.03 1.50e+00 4.44e-01 3.62e+01 angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 112.29 107.22 5.07 9.40e-01 1.13e+00 2.91e+01 angle pdb=" O3' DC X 80 " pdb=" C3' DC X 80 " pdb=" C2' DC X 80 " ideal model delta sigma weight residual 111.50 118.07 -6.57 1.50e+00 4.44e-01 1.92e+01 ... (remaining 33903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13594 17.86 - 35.71: 776 35.71 - 53.57: 322 53.57 - 71.42: 54 71.42 - 89.28: 9 Dihedral angle restraints: 14755 sinusoidal: 6466 harmonic: 8289 Sorted by residual: dihedral pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual 122.80 131.57 -8.77 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" C MET C 665 " pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual -122.60 -131.28 8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CA SER C 419 " pdb=" C SER C 419 " pdb=" N PRO C 420 " pdb=" CA PRO C 420 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 14752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3556 0.093 - 0.187: 165 0.187 - 0.280: 4 0.280 - 0.373: 2 0.373 - 0.466: 2 Chirality restraints: 3729 Sorted by residual: chirality pdb=" CA MET C 665 " pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CB MET C 665 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C4' DT X 81 " pdb=" C5' DT X 81 " pdb=" O4' DT X 81 " pdb=" C3' DT X 81 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA LEU C 664 " pdb=" N LEU C 664 " pdb=" C LEU C 664 " pdb=" CB LEU C 664 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3726 not shown) Planarity restraints: 4219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG X 79 " -0.021 2.00e-02 2.50e+03 1.57e-02 7.44e+00 pdb=" N9 DG X 79 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DG X 79 " 0.043 2.00e-02 2.50e+03 pdb=" N7 DG X 79 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG X 79 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG X 79 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG X 79 " -0.018 2.00e-02 2.50e+03 pdb=" N1 DG X 79 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG X 79 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG X 79 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DG X 79 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG X 79 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.040 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 420 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 304 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO B 305 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.031 5.00e-02 4.00e+02 ... (remaining 4216 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3238 2.76 - 3.30: 21004 3.30 - 3.83: 40288 3.83 - 4.37: 45781 4.37 - 4.90: 78345 Nonbonded interactions: 188656 Sorted by model distance: nonbonded pdb=" NH2 ARG C 668 " pdb=" OD1 ASP C 711 " model vdw 2.227 2.520 nonbonded pdb=" O ILE C 670 " pdb=" OG SER C 722 " model vdw 2.271 2.440 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.304 2.496 nonbonded pdb=" O THR D 533 " pdb=" OG1 THR D 533 " model vdw 2.314 2.440 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.329 2.440 ... (remaining 188651 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.390 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 69.760 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.072 24774 Z= 0.176 Angle : 0.580 11.586 33908 Z= 0.355 Chirality : 0.042 0.466 3729 Planarity : 0.005 0.059 4219 Dihedral : 13.428 89.279 9383 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.57 % Allowed : 5.38 % Favored : 92.05 % 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: -3.60 (0.12), residues: 2837 helix: -2.56 (0.09), residues: 1389 sheet: -1.02 (0.28), residues: 301 loop : -2.35 (0.14), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 652 HIS 0.004 0.000 HIS D 256 PHE 0.015 0.001 PHE B1023 TYR 0.012 0.001 TYR C 190 ARG 0.004 0.000 ARG B 761 *********************** 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 730 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 668 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 LEU cc_start: 0.8762 (mp) cc_final: 0.8143 (mt) REVERT: B 234 GLN cc_start: 0.8943 (tt0) cc_final: 0.8689 (mm110) REVERT: B 610 ASN cc_start: 0.8781 (t0) cc_final: 0.8494 (t0) REVERT: B 646 ASP cc_start: 0.8629 (t0) cc_final: 0.8367 (t0) REVERT: B 832 ASP cc_start: 0.7810 (m-30) cc_final: 0.7417 (m-30) REVERT: B 1053 LEU cc_start: 0.5128 (OUTLIER) cc_final: 0.4508 (mp) REVERT: B 1079 LEU cc_start: 0.9064 (tp) cc_final: 0.8714 (tp) REVERT: C 509 ASP cc_start: 0.7973 (t0) cc_final: 0.7457 (t0) REVERT: C 548 LEU cc_start: 0.9305 (tp) cc_final: 0.9074 (tp) REVERT: C 554 SER cc_start: 0.8234 (p) cc_final: 0.7935 (t) REVERT: C 978 MET cc_start: 0.8942 (tpp) cc_final: 0.8555 (tpp) REVERT: D 68 LEU cc_start: 0.6554 (pp) cc_final: 0.6197 (mt) REVERT: D 116 GLU cc_start: 0.8494 (tp30) cc_final: 0.8283 (tp30) REVERT: D 350 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6878 (t70) REVERT: D 404 TYR cc_start: 0.8411 (t80) cc_final: 0.7034 (t80) REVERT: D 462 MET cc_start: 0.8349 (mmt) cc_final: 0.7921 (mmp) outliers start: 62 outliers final: 14 residues processed: 708 average time/residue: 0.3936 time to fit residues: 415.5865 Evaluate side-chains 345 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 329 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 THR 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 1053 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 502 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 262 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 150 GLN B 181 GLN B 222 HIS B 261 ASN B 278 ASN B 455 ASN B 458 ASN B 463 GLN B 594 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN B 765 GLN B 769 HIS B 834 HIS B 848 GLN B 943 HIS B 944 GLN B1003 ASN B1072 HIS B1134 HIS C 6 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 264 GLN C 570 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN C 724 GLN C 749 GLN C 759 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN C 951 GLN C1110 GLN D 22 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 115 ASN D 251 GLN D 455 ASN D 469 HIS D 542 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24774 Z= 0.327 Angle : 0.652 10.655 33908 Z= 0.332 Chirality : 0.042 0.206 3729 Planarity : 0.005 0.055 4219 Dihedral : 14.538 87.713 3874 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.02 % Allowed : 12.26 % Favored : 83.73 % 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: -1.13 (0.14), residues: 2837 helix: 0.04 (0.13), residues: 1412 sheet: -0.36 (0.30), residues: 274 loop : -1.80 (0.16), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 574 HIS 0.007 0.001 HIS C 390 PHE 0.018 0.002 PHE D 145 TYR 0.022 0.002 TYR B1111 ARG 0.009 0.001 ARG D 331 *********************** 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 393 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 296 time to evaluate : 2.331 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: B 146 MET cc_start: 0.7662 (mmm) cc_final: 0.7424 (mmm) REVERT: B 234 GLN cc_start: 0.9006 (tt0) cc_final: 0.8716 (mm110) REVERT: B 491 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.5521 (m-80) REVERT: B 758 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.8935 (p) REVERT: C 42 MET cc_start: 0.8657 (tmm) cc_final: 0.8273 (tmm) REVERT: C 230 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9238 (tt) REVERT: C 475 ASP cc_start: 0.8396 (m-30) cc_final: 0.8137 (m-30) REVERT: C 528 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9188 (mm) REVERT: C 548 LEU cc_start: 0.9492 (tp) cc_final: 0.9249 (tp) REVERT: C 569 MET cc_start: 0.7638 (tpp) cc_final: 0.7407 (tpt) REVERT: C 1072 LEU cc_start: 0.8613 (mt) cc_final: 0.8400 (mt) REVERT: D 68 LEU cc_start: 0.6517 (pp) cc_final: 0.6037 (mt) REVERT: D 332 LEU cc_start: 0.8923 (mt) cc_final: 0.8465 (mt) REVERT: D 449 PHE cc_start: 0.8298 (m-10) cc_final: 0.7998 (m-80) REVERT: D 483 MET cc_start: 0.7950 (ttp) cc_final: 0.7579 (ttp) REVERT: D 504 ARG cc_start: 0.8271 (tpt90) cc_final: 0.7913 (tpp80) REVERT: D 564 GLU cc_start: 0.8339 (mp0) cc_final: 0.8033 (mp0) outliers start: 97 outliers final: 55 residues processed: 366 average time/residue: 0.3623 time to fit residues: 208.9941 Evaluate side-chains 299 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1079 MET Chi-restraints excluded: chain C residue 1109 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 262 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B1133 HIS B1153 GLN C 8 ASN ** C 38 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** C 886 ASN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24774 Z= 0.253 Angle : 0.568 13.235 33908 Z= 0.289 Chirality : 0.040 0.156 3729 Planarity : 0.004 0.049 4219 Dihedral : 14.551 89.467 3862 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.77 % Allowed : 12.88 % Favored : 83.35 % 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: -0.13 (0.15), residues: 2837 helix: 1.01 (0.14), residues: 1408 sheet: -0.17 (0.29), residues: 290 loop : -1.46 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 901 HIS 0.005 0.001 HIS B 705 PHE 0.010 0.001 PHE C 62 TYR 0.021 0.002 TYR C 434 ARG 0.003 0.000 ARG B 728 *********************** 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 347 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 256 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: B 129 ILE cc_start: 0.8824 (mt) cc_final: 0.8563 (mt) REVERT: B 146 MET cc_start: 0.7637 (mmm) cc_final: 0.7334 (mmm) REVERT: B 234 GLN cc_start: 0.9016 (tt0) cc_final: 0.8706 (mm110) REVERT: B 304 THR cc_start: 0.7199 (OUTLIER) cc_final: 0.6967 (p) REVERT: B 411 LEU cc_start: 0.9404 (mt) cc_final: 0.9174 (mp) REVERT: B 491 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.5715 (m-80) REVERT: B 758 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8910 (p) REVERT: B 947 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6475 (ptp-170) REVERT: B 959 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 1102 MET cc_start: 0.7838 (tpt) cc_final: 0.7557 (tmm) REVERT: C 47 GLN cc_start: 0.8922 (tt0) cc_final: 0.8656 (tt0) REVERT: C 383 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7759 (tt0) REVERT: C 475 ASP cc_start: 0.8339 (m-30) cc_final: 0.8101 (m-30) REVERT: C 528 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9357 (mm) REVERT: C 548 LEU cc_start: 0.9511 (tp) cc_final: 0.9293 (tp) REVERT: C 665 MET cc_start: 0.8445 (mtp) cc_final: 0.8157 (ttm) REVERT: C 817 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8235 (m90) REVERT: C 924 MET cc_start: 0.8912 (mmt) cc_final: 0.8539 (mmp) REVERT: D 504 ARG cc_start: 0.8202 (tpt90) cc_final: 0.7836 (tpp80) REVERT: D 594 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8473 (p) outliers start: 91 outliers final: 58 residues processed: 318 average time/residue: 0.3289 time to fit residues: 172.6713 Evaluate side-chains 292 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 226 time to evaluate : 2.538 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1079 MET Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 40.0000 chunk 197 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 250 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 GLN C1110 GLN D 530 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 24774 Z= 0.392 Angle : 0.655 10.530 33908 Z= 0.332 Chirality : 0.042 0.182 3729 Planarity : 0.004 0.037 4219 Dihedral : 14.821 89.478 3862 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.35 % Allowed : 13.50 % Favored : 82.15 % 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: 0.17 (0.16), residues: 2837 helix: 1.25 (0.14), residues: 1409 sheet: -0.26 (0.29), residues: 294 loop : -1.23 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 248 HIS 0.005 0.001 HIS C 390 PHE 0.032 0.002 PHE D 386 TYR 0.017 0.002 TYR C 190 ARG 0.004 0.001 ARG C 265 *********************** 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 340 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 235 time to evaluate : 2.850 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: 0.7733 (mmm) cc_final: 0.7416 (mmm) REVERT: B 234 GLN cc_start: 0.9018 (tt0) cc_final: 0.8679 (mm110) REVERT: B 288 LYS cc_start: 0.7488 (ttmt) cc_final: 0.7144 (tptp) REVERT: B 304 THR cc_start: 0.6945 (OUTLIER) cc_final: 0.6680 (p) REVERT: B 491 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.5330 (m-80) REVERT: B 758 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.8972 (p) REVERT: B 1061 MET cc_start: 0.7168 (mpp) cc_final: 0.6935 (mmt) REVERT: C 475 ASP cc_start: 0.8452 (m-30) cc_final: 0.8229 (m-30) REVERT: C 665 MET cc_start: 0.8588 (mtp) cc_final: 0.8221 (ttm) REVERT: C 680 MET cc_start: 0.9293 (mmm) cc_final: 0.9023 (mmt) REVERT: C 817 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8289 (m90) REVERT: C 1079 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8775 (pmm) REVERT: C 1102 MET cc_start: 0.9161 (tpp) cc_final: 0.8883 (tpp) REVERT: D 462 MET cc_start: 0.8586 (mmm) cc_final: 0.8226 (mmp) outliers start: 105 outliers final: 72 residues processed: 309 average time/residue: 0.3275 time to fit residues: 167.2815 Evaluate side-chains 288 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 211 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1079 MET Chi-restraints excluded: chain C residue 1109 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN B 689 HIS C 8 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 510 ASN C 545 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24774 Z= 0.339 Angle : 0.613 11.040 33908 Z= 0.311 Chirality : 0.041 0.145 3729 Planarity : 0.004 0.040 4219 Dihedral : 14.949 89.863 3862 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.06 % Allowed : 14.58 % Favored : 81.37 % 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: 0.38 (0.16), residues: 2837 helix: 1.44 (0.14), residues: 1409 sheet: -0.22 (0.30), residues: 282 loop : -1.13 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 901 HIS 0.005 0.001 HIS C 390 PHE 0.020 0.001 PHE D 386 TYR 0.026 0.002 TYR C 434 ARG 0.006 0.001 ARG C 491 *********************** 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 329 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 231 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7752 (mmm) cc_final: 0.7441 (mmm) REVERT: B 234 GLN cc_start: 0.9014 (tt0) cc_final: 0.8685 (mm110) REVERT: B 288 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7253 (tptp) REVERT: B 304 THR cc_start: 0.6816 (OUTLIER) cc_final: 0.6565 (p) REVERT: B 414 ASP cc_start: 0.8203 (t0) cc_final: 0.7957 (t0) REVERT: B 595 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8119 (mt-10) REVERT: B 758 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.8939 (p) REVERT: B 761 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7415 (mtt90) REVERT: B 947 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6107 (ptp90) REVERT: B 959 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8452 (t80) REVERT: C 17 MET cc_start: 0.9074 (tmm) cc_final: 0.8527 (ptp) REVERT: C 42 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8046 (tmm) REVERT: C 219 LEU cc_start: 0.8604 (tp) cc_final: 0.8239 (tt) REVERT: C 362 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: C 383 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 665 MET cc_start: 0.8624 (mtp) cc_final: 0.8407 (ttp) REVERT: C 667 MET cc_start: 0.8589 (mtm) cc_final: 0.8171 (mtt) REVERT: C 817 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8281 (m90) REVERT: C 1079 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8795 (pmm) REVERT: D 35 VAL cc_start: 0.9637 (OUTLIER) cc_final: 0.9428 (p) REVERT: D 504 ARG cc_start: 0.8269 (tpt90) cc_final: 0.7928 (tpp80) outliers start: 98 outliers final: 60 residues processed: 299 average time/residue: 0.3246 time to fit residues: 158.0772 Evaluate side-chains 282 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 212 time to evaluate : 2.387 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1079 MET Chi-restraints excluded: chain C residue 1109 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 303 SER 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 425 ARG Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN C 8 ASN ** C 38 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** C1053 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24774 Z= 0.319 Angle : 0.605 10.749 33908 Z= 0.305 Chirality : 0.041 0.206 3729 Planarity : 0.004 0.041 4219 Dihedral : 15.019 89.970 3860 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.18 % Allowed : 15.16 % Favored : 80.66 % 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: 1.54 (0.14), residues: 1419 sheet: -0.19 (0.30), residues: 285 loop : -1.11 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 638 HIS 0.005 0.001 HIS C 390 PHE 0.014 0.001 PHE D 386 TYR 0.023 0.002 TYR C 434 ARG 0.006 0.000 ARG C 491 *********************** 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 327 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 226 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 GLN cc_start: 0.9002 (tt0) cc_final: 0.8667 (mm110) REVERT: B 288 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7306 (tptp) REVERT: B 304 THR cc_start: 0.6670 (OUTLIER) cc_final: 0.6437 (p) REVERT: B 414 ASP cc_start: 0.8174 (t0) cc_final: 0.7898 (t0) REVERT: B 589 GLU cc_start: 0.7850 (tt0) cc_final: 0.7610 (pt0) REVERT: B 595 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 599 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9291 (mp) REVERT: B 758 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.8940 (p) REVERT: B 761 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7507 (mtt90) REVERT: B 978 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8018 (mm-30) REVERT: C 17 MET cc_start: 0.9012 (tmm) cc_final: 0.8488 (ptp) REVERT: C 42 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8033 (tmm) REVERT: C 383 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7524 (tm-30) REVERT: C 1079 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8818 (pmm) REVERT: D 35 VAL cc_start: 0.9642 (OUTLIER) cc_final: 0.9439 (p) outliers start: 101 outliers final: 72 residues processed: 299 average time/residue: 0.3268 time to fit residues: 157.2554 Evaluate side-chains 291 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 212 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1053 GLN Chi-restraints excluded: chain C residue 1079 MET Chi-restraints excluded: chain C residue 1109 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 ASN C 920 GLN D 518 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24774 Z= 0.170 Angle : 0.557 11.039 33908 Z= 0.277 Chirality : 0.039 0.346 3729 Planarity : 0.003 0.039 4219 Dihedral : 14.931 88.541 3860 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.35 % Allowed : 16.07 % Favored : 80.58 % 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: 0.74 (0.16), residues: 2837 helix: 1.80 (0.14), residues: 1420 sheet: -0.06 (0.30), residues: 287 loop : -1.08 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 401 HIS 0.005 0.001 HIS C 817 PHE 0.021 0.001 PHE D 386 TYR 0.022 0.001 TYR C 434 ARG 0.007 0.000 ARG C 491 *********************** 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 317 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 236 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7540 (mmp) cc_final: 0.7135 (mmm) REVERT: B 234 GLN cc_start: 0.8998 (tt0) cc_final: 0.8680 (mm110) REVERT: B 288 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7302 (tptp) REVERT: B 304 THR cc_start: 0.6644 (OUTLIER) cc_final: 0.6411 (p) REVERT: B 414 ASP cc_start: 0.8169 (t0) cc_final: 0.7860 (t0) REVERT: B 589 GLU cc_start: 0.7719 (tt0) cc_final: 0.7454 (pt0) REVERT: B 595 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8066 (mt-10) REVERT: B 758 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 959 PHE cc_start: 0.8519 (t80) cc_final: 0.8252 (t80) REVERT: B 1098 MET cc_start: 0.5740 (mtm) cc_final: 0.5532 (mmt) REVERT: C 17 MET cc_start: 0.9036 (tmm) cc_final: 0.8440 (ptp) REVERT: C 219 LEU cc_start: 0.8420 (tp) cc_final: 0.7999 (tt) REVERT: C 362 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: C 383 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 507 ASP cc_start: 0.8326 (t0) cc_final: 0.8036 (t0) REVERT: C 885 LEU cc_start: 0.9259 (tp) cc_final: 0.8991 (mt) REVERT: C 1079 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8672 (pmm) REVERT: D 35 VAL cc_start: 0.9637 (OUTLIER) cc_final: 0.9432 (p) REVERT: D 449 PHE cc_start: 0.8409 (m-10) cc_final: 0.7841 (m-80) outliers start: 81 outliers final: 58 residues processed: 292 average time/residue: 0.3494 time to fit residues: 166.5444 Evaluate side-chains 285 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 222 time to evaluate : 2.749 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1079 MET Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 530 HIS Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 0.0980 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 448 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 817 HIS C 881 ASN C 920 GLN C1054 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 24774 Z= 0.154 Angle : 0.541 11.010 33908 Z= 0.271 Chirality : 0.039 0.198 3729 Planarity : 0.003 0.037 4219 Dihedral : 14.836 87.007 3860 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.98 % Allowed : 16.60 % Favored : 80.41 % 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: 0.91 (0.16), residues: 2837 helix: 1.96 (0.14), residues: 1418 sheet: -0.05 (0.31), residues: 270 loop : -0.99 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 401 HIS 0.003 0.001 HIS C 390 PHE 0.019 0.001 PHE B1070 TYR 0.021 0.001 TYR D 580 ARG 0.008 0.000 ARG C 491 *********************** 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 315 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 243 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 GLN cc_start: 0.8993 (tt0) cc_final: 0.8686 (mm110) REVERT: B 288 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7277 (tptp) REVERT: B 304 THR cc_start: 0.6750 (OUTLIER) cc_final: 0.6503 (p) REVERT: B 414 ASP cc_start: 0.8159 (t0) cc_final: 0.7834 (t0) REVERT: B 595 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8088 (mt-10) REVERT: B 758 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8891 (p) REVERT: B 947 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6069 (ptp90) REVERT: B 959 PHE cc_start: 0.8542 (t80) cc_final: 0.8212 (t80) REVERT: C 8 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8773 (m110) REVERT: C 219 LEU cc_start: 0.8383 (tp) cc_final: 0.7999 (tt) REVERT: C 362 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: C 383 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 507 ASP cc_start: 0.8356 (t0) cc_final: 0.8062 (t0) REVERT: C 688 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: C 885 LEU cc_start: 0.9283 (tp) cc_final: 0.9011 (mt) REVERT: D 35 VAL cc_start: 0.9626 (OUTLIER) cc_final: 0.9416 (p) REVERT: D 600 LEU cc_start: 0.8893 (mt) cc_final: 0.8586 (mt) outliers start: 72 outliers final: 52 residues processed: 291 average time/residue: 0.3231 time to fit residues: 153.8278 Evaluate side-chains 289 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 2.601 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 586 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 30.0000 chunk 266 optimal weight: 9.9990 chunk 243 optimal weight: 0.9980 chunk 259 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 245 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 881 ASN C 920 GLN D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24774 Z= 0.256 Angle : 0.583 11.075 33908 Z= 0.291 Chirality : 0.040 0.201 3729 Planarity : 0.003 0.037 4219 Dihedral : 14.882 89.665 3860 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.11 % Allowed : 16.73 % Favored : 80.17 % 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: 0.91 (0.16), residues: 2837 helix: 1.95 (0.14), residues: 1426 sheet: 0.05 (0.31), residues: 280 loop : -1.04 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 534 HIS 0.007 0.001 HIS C 6 PHE 0.016 0.001 PHE B 386 TYR 0.026 0.001 TYR D 580 ARG 0.007 0.000 ARG C 491 *********************** 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 305 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 230 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7560 (mmm) cc_final: 0.7251 (mmm) REVERT: B 234 GLN cc_start: 0.9009 (tt0) cc_final: 0.8699 (mm110) REVERT: B 288 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7232 (tptp) REVERT: B 304 THR cc_start: 0.6708 (OUTLIER) cc_final: 0.6457 (p) REVERT: B 414 ASP cc_start: 0.8150 (t0) cc_final: 0.7867 (t0) REVERT: B 758 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.8945 (p) REVERT: B 959 PHE cc_start: 0.8606 (t80) cc_final: 0.8251 (t80) REVERT: C 8 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8744 (m110) REVERT: C 17 MET cc_start: 0.9137 (tmm) cc_final: 0.8733 (ptp) REVERT: C 42 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8594 (tmm) REVERT: C 219 LEU cc_start: 0.8325 (tp) cc_final: 0.7951 (tt) REVERT: C 507 ASP cc_start: 0.8431 (t0) cc_final: 0.8107 (t0) REVERT: C 688 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: D 35 VAL cc_start: 0.9640 (OUTLIER) cc_final: 0.9436 (p) REVERT: D 449 PHE cc_start: 0.8370 (m-10) cc_final: 0.7975 (m-80) REVERT: D 493 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8251 (mt) outliers start: 75 outliers final: 58 residues processed: 282 average time/residue: 0.3240 time to fit residues: 151.5174 Evaluate side-chains 286 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 221 time to evaluate : 2.819 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 530 HIS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 0.0470 chunk 274 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 190 optimal weight: 0.0170 chunk 287 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 229 optimal weight: 0.3980 chunk 23 optimal weight: 0.0870 chunk 177 optimal weight: 0.0470 chunk 140 optimal weight: 8.9990 overall best weight: 0.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 742 HIS C 8 ASN ** C 59 ASN ** 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** C 725 GLN C 881 ASN C 920 GLN D 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24774 Z= 0.144 Angle : 0.568 16.595 33908 Z= 0.280 Chirality : 0.039 0.332 3729 Planarity : 0.003 0.037 4219 Dihedral : 14.781 86.779 3860 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.95 % Allowed : 17.85 % Favored : 80.21 % 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: 1.05 (0.16), residues: 2837 helix: 2.07 (0.14), residues: 1417 sheet: -0.05 (0.31), residues: 282 loop : -0.91 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 534 HIS 0.005 0.001 HIS C 6 PHE 0.051 0.001 PHE D 386 TYR 0.022 0.001 TYR D 580 ARG 0.009 0.000 ARG C 491 ********************** 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 303 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7453 (mmm) cc_final: 0.7178 (mmm) REVERT: B 234 GLN cc_start: 0.9006 (tt0) cc_final: 0.8727 (mm110) REVERT: B 304 THR cc_start: 0.6730 (OUTLIER) cc_final: 0.6489 (p) REVERT: B 414 ASP cc_start: 0.8116 (t0) cc_final: 0.7809 (t0) REVERT: B 728 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.8058 (tmm-80) REVERT: B 758 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8871 (p) REVERT: B 947 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6103 (ptp90) REVERT: B 959 PHE cc_start: 0.8563 (t80) cc_final: 0.8203 (t80) REVERT: C 17 MET cc_start: 0.9133 (tmm) cc_final: 0.8545 (ptp) REVERT: C 219 LEU cc_start: 0.8245 (tp) cc_final: 0.7936 (tt) REVERT: C 362 ASP cc_start: 0.8394 (m-30) cc_final: 0.8118 (m-30) REVERT: C 383 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 507 ASP cc_start: 0.8395 (t0) cc_final: 0.8089 (t0) REVERT: C 688 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: C 885 LEU cc_start: 0.9255 (tp) cc_final: 0.9025 (mt) REVERT: D 35 VAL cc_start: 0.9601 (OUTLIER) cc_final: 0.9384 (p) REVERT: D 449 PHE cc_start: 0.8342 (m-10) cc_final: 0.8049 (m-80) REVERT: D 493 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8697 (pp) outliers start: 47 outliers final: 34 residues processed: 292 average time/residue: 0.3204 time to fit residues: 154.1541 Evaluate side-chains 276 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 236 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 ASN ** 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** C 614 GLN C 725 GLN ** C 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062406 restraints weight = 74234.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064415 restraints weight = 39593.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065749 restraints weight = 26364.599| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 24774 Z= 0.365 Angle : 0.659 12.847 33908 Z= 0.326 Chirality : 0.043 0.356 3729 Planarity : 0.004 0.036 4219 Dihedral : 14.940 89.677 3860 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.48 % Allowed : 17.81 % Favored : 79.71 % 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: 0.89 (0.16), residues: 2837 helix: 1.90 (0.14), residues: 1430 sheet: 0.03 (0.31), residues: 281 loop : -1.00 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 534 HIS 0.006 0.001 HIS B 742 PHE 0.024 0.002 PHE D 386 TYR 0.026 0.002 TYR D 580 ARG 0.007 0.001 ARG C 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4524.20 seconds wall clock time: 82 minutes 27.03 seconds (4947.03 seconds total)