Starting phenix.real_space_refine on Thu Feb 15 19:32:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5a_15163/02_2024/8a5a_15163_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5a_15163/02_2024/8a5a_15163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5a_15163/02_2024/8a5a_15163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5a_15163/02_2024/8a5a_15163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5a_15163/02_2024/8a5a_15163_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5a_15163/02_2024/8a5a_15163_updated.pdb" } resolution = 3.3 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= 0.006 sd= 0.157 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 49 5.16 5 C 8361 2.51 5 N 2238 2.21 5 O 2531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 482": "NH1" <-> "NH2" Residue "G ASP 527": "OD1" <-> "OD2" Residue "G PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 533": "NH1" <-> "NH2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "U GLU 183": "OE1" <-> "OE2" Residue "U PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 219": "NH1" <-> "NH2" Residue "U ASP 220": "OD1" <-> "OD2" Residue "U ASP 264": "OD1" <-> "OD2" Residue "U ASP 303": "OD1" <-> "OD2" Residue "U PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 331": "OE1" <-> "OE2" Residue "U PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 380": "OD1" <-> "OD2" Residue "U TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 484": "OE1" <-> "OE2" Residue "U GLU 563": "OE1" <-> "OE2" Residue "U TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 602": "OD1" <-> "OD2" Residue "U PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 639": "OD1" <-> "OD2" Residue "U PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 668": "OD1" <-> "OD2" Residue "U TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 809": "OE1" <-> "OE2" Residue "U GLU 822": "OE1" <-> "OE2" Residue "U ARG 834": "NH1" <-> "NH2" Residue "U ARG 871": "NH1" <-> "NH2" Residue "V GLU 4": "OE1" <-> "OE2" Residue "V PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 95": "NH1" <-> "NH2" Residue "V ASP 154": "OD1" <-> "OD2" Residue "V ASP 157": "OD1" <-> "OD2" Residue "V ASP 179": "OD1" <-> "OD2" Residue "V ARG 183": "NH1" <-> "NH2" Residue "V ARG 196": "NH1" <-> "NH2" Residue "V ARG 206": "NH1" <-> "NH2" Residue "V ARG 210": "NH1" <-> "NH2" Residue "V ASP 211": "OD1" <-> "OD2" Residue "V TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 222": "OD1" <-> "OD2" Residue "V TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 275": "OD1" <-> "OD2" Residue "V GLU 292": "OE1" <-> "OE2" Residue "W TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "W ASP 84": "OD1" <-> "OD2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 241": "OE1" <-> "OE2" Residue "W ARG 268": "NH1" <-> "NH2" Residue "W GLU 271": "OE1" <-> "OE2" Residue "W PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 281": "OD1" <-> "OD2" Residue "W GLU 291": "OE1" <-> "OE2" Residue "W PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 474": "OE1" <-> "OE2" Residue "W ARG 489": "NH1" <-> "NH2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 66": "NH1" <-> "NH2" Residue "X ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13191 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 938 Classifications: {'peptide': 110} Link IDs: {'TRANS': 109} Chain: "U" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5582 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 656} Chain breaks: 1 Chain: "V" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3398 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 347 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.17, per 1000 atoms: 0.54 Number of scatterers: 13191 At special positions: 0 Unit cell: (100.605, 99.546, 163.086, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 9 15.00 Mg 3 11.99 O 2531 8.00 N 2238 7.00 C 8361 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: 6.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 13 sheets defined 45.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'G' and resid 459 through 481 Processing helix chain 'G' and resid 485 through 518 removed outlier: 4.117A pdb=" N LYS G 515 " --> pdb=" O ALA G 511 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS G 516 " --> pdb=" O ARG G 512 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN G 518 " --> pdb=" O ALA G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 559 Processing helix chain 'U' and resid 166 through 178 removed outlier: 3.550A pdb=" N LYS U 172 " --> pdb=" O GLU U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 216 through 227 Processing helix chain 'U' and resid 299 through 301 No H-bonds generated for 'chain 'U' and resid 299 through 301' Processing helix chain 'U' and resid 321 through 340 Processing helix chain 'U' and resid 349 through 359 removed outlier: 3.668A pdb=" N ASN U 359 " --> pdb=" O SER U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 369 No H-bonds generated for 'chain 'U' and resid 367 through 369' Processing helix chain 'U' and resid 386 through 391 Processing helix chain 'U' and resid 418 through 433 Processing helix chain 'U' and resid 445 through 447 No H-bonds generated for 'chain 'U' and resid 445 through 447' Processing helix chain 'U' and resid 460 through 471 removed outlier: 3.610A pdb=" N ARG U 468 " --> pdb=" O GLU U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 484 through 492 Processing helix chain 'U' and resid 520 through 522 No H-bonds generated for 'chain 'U' and resid 520 through 522' Processing helix chain 'U' and resid 530 through 544 Processing helix chain 'U' and resid 556 through 569 removed outlier: 4.180A pdb=" N LEU U 561 " --> pdb=" O HIS U 557 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG U 564 " --> pdb=" O LEU U 560 " (cutoff:3.500A) Processing helix chain 'U' and resid 574 through 576 No H-bonds generated for 'chain 'U' and resid 574 through 576' Processing helix chain 'U' and resid 602 through 612 removed outlier: 3.600A pdb=" N LEU U 606 " --> pdb=" O GLU U 603 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA U 607 " --> pdb=" O VAL U 604 " (cutoff:3.500A) Proline residue: U 608 - end of helix Processing helix chain 'U' and resid 614 through 620 removed outlier: 3.776A pdb=" N ILE U 620 " --> pdb=" O PHE U 617 " (cutoff:3.500A) Processing helix chain 'U' and resid 630 through 632 No H-bonds generated for 'chain 'U' and resid 630 through 632' Processing helix chain 'U' and resid 651 through 657 Processing helix chain 'U' and resid 662 through 664 No H-bonds generated for 'chain 'U' and resid 662 through 664' Processing helix chain 'U' and resid 668 through 687 removed outlier: 3.821A pdb=" N ASP U 677 " --> pdb=" O ASN U 673 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N HIS U 679 " --> pdb=" O ILE U 675 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN U 680 " --> pdb=" O LEU U 676 " (cutoff:3.500A) Processing helix chain 'U' and resid 689 through 692 No H-bonds generated for 'chain 'U' and resid 689 through 692' Processing helix chain 'U' and resid 703 through 717 removed outlier: 3.958A pdb=" N ASN U 713 " --> pdb=" O GLN U 709 " (cutoff:3.500A) Processing helix chain 'U' and resid 720 through 727 removed outlier: 3.740A pdb=" N ASN U 724 " --> pdb=" O THR U 721 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR U 727 " --> pdb=" O ASN U 724 " (cutoff:3.500A) Processing helix chain 'U' and resid 735 through 738 Processing helix chain 'U' and resid 742 through 753 Processing helix chain 'U' and resid 763 through 780 Processing helix chain 'U' and resid 789 through 815 Processing helix chain 'U' and resid 819 through 822 Processing helix chain 'U' and resid 841 through 850 removed outlier: 3.629A pdb=" N ALA U 846 " --> pdb=" O ILE U 842 " (cutoff:3.500A) Processing helix chain 'U' and resid 853 through 857 removed outlier: 3.560A pdb=" N GLU U 856 " --> pdb=" O LYS U 853 " (cutoff:3.500A) Processing helix chain 'U' and resid 862 through 876 removed outlier: 4.050A pdb=" N VAL U 867 " --> pdb=" O SER U 863 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N SER U 870 " --> pdb=" O ASP U 866 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ARG U 871 " --> pdb=" O VAL U 867 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE U 872 " --> pdb=" O HIS U 868 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU U 873 " --> pdb=" O GLY U 869 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN U 874 " --> pdb=" O SER U 870 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR U 875 " --> pdb=" O ARG U 871 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'V' and resid 62 through 64 No H-bonds generated for 'chain 'V' and resid 62 through 64' Processing helix chain 'V' and resid 79 through 91 removed outlier: 3.777A pdb=" N LYS V 84 " --> pdb=" O ASP V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 100 No H-bonds generated for 'chain 'V' and resid 98 through 100' Processing helix chain 'V' and resid 113 through 127 removed outlier: 3.685A pdb=" N PHE V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 137 through 145 removed outlier: 3.793A pdb=" N SER V 145 " --> pdb=" O SER V 141 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 174 No H-bonds generated for 'chain 'V' and resid 172 through 174' Processing helix chain 'V' and resid 182 through 196 Processing helix chain 'V' and resid 203 through 216 removed outlier: 3.754A pdb=" N GLU V 207 " --> pdb=" O THR V 203 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE V 208 " --> pdb=" O ALA V 204 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP V 211 " --> pdb=" O GLU V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 223 through 232 Processing helix chain 'V' and resid 252 through 261 removed outlier: 3.789A pdb=" N ARG V 256 " --> pdb=" O GLU V 253 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA V 257 " --> pdb=" O ARG V 254 " (cutoff:3.500A) Proline residue: V 258 - end of helix Processing helix chain 'V' and resid 264 through 267 Processing helix chain 'V' and resid 274 through 284 Processing helix chain 'V' and resid 290 through 294 Processing helix chain 'V' and resid 302 through 305 Processing helix chain 'V' and resid 309 through 320 Processing helix chain 'V' and resid 338 through 348 removed outlier: 3.508A pdb=" N GLY V 343 " --> pdb=" O VAL V 339 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER V 348 " --> pdb=" O SER V 344 " (cutoff:3.500A) Processing helix chain 'V' and resid 352 through 355 No H-bonds generated for 'chain 'V' and resid 352 through 355' Processing helix chain 'V' and resid 359 through 372 Proline residue: V 367 - end of helix removed outlier: 5.000A pdb=" N VAL V 370 " --> pdb=" O GLY V 366 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N HIS V 371 " --> pdb=" O PRO V 367 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS V 372 " --> pdb=" O SER V 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 96 Processing helix chain 'W' and resid 118 through 129 removed outlier: 3.936A pdb=" N LEU W 125 " --> pdb=" O ARG W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 150 Processing helix chain 'W' and resid 187 through 198 removed outlier: 3.751A pdb=" N LEU W 198 " --> pdb=" O ILE W 194 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 208 No H-bonds generated for 'chain 'W' and resid 206 through 208' Processing helix chain 'W' and resid 227 through 235 Processing helix chain 'W' and resid 238 through 245 Processing helix chain 'W' and resid 259 through 264 removed outlier: 3.772A pdb=" N SER W 264 " --> pdb=" O THR W 260 " (cutoff:3.500A) Processing helix chain 'W' and resid 282 through 292 removed outlier: 4.009A pdb=" N ALA W 289 " --> pdb=" O ARG W 285 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU W 291 " --> pdb=" O GLY W 287 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU W 292 " --> pdb=" O PHE W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 308 through 310 No H-bonds generated for 'chain 'W' and resid 308 through 310' Processing helix chain 'W' and resid 385 through 395 removed outlier: 3.526A pdb=" N ILE W 393 " --> pdb=" O VAL W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 398 through 407 removed outlier: 4.709A pdb=" N ALA W 402 " --> pdb=" O VAL W 398 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR W 403 " --> pdb=" O ASP W 399 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN W 407 " --> pdb=" O THR W 403 " (cutoff:3.500A) Processing helix chain 'W' and resid 413 through 415 No H-bonds generated for 'chain 'W' and resid 413 through 415' Processing helix chain 'W' and resid 420 through 431 Processing helix chain 'W' and resid 446 through 461 removed outlier: 4.669A pdb=" N GLN W 451 " --> pdb=" O ARG W 448 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER W 452 " --> pdb=" O GLN W 449 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU W 454 " --> pdb=" O GLN W 451 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR W 460 " --> pdb=" O SER W 457 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 468 Processing helix chain 'W' and resid 472 through 478 Processing helix chain 'W' and resid 480 through 486 removed outlier: 3.938A pdb=" N ASN W 485 " --> pdb=" O GLU W 481 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 72 removed outlier: 3.971A pdb=" N GLU X 71 " --> pdb=" O ASP X 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'U' and resid 289 through 292 removed outlier: 6.210A pdb=" N LYS U 449 " --> pdb=" O ILE U 269 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE U 271 " --> pdb=" O LYS U 449 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL U 451 " --> pdb=" O ILE U 271 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA U 478 " --> pdb=" O VAL U 450 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU U 452 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA U 480 " --> pdb=" O LEU U 452 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE U 454 " --> pdb=" O ALA U 480 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE U 482 " --> pdb=" O ILE U 454 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'U' and resid 295 through 298 Processing sheet with id= C, first strand: chain 'U' and resid 363 through 365 removed outlier: 3.864A pdb=" N THR U 593 " --> pdb=" O ILE U 365 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE U 584 " --> pdb=" O TYR U 596 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'U' and resid 730 through 732 removed outlier: 6.192A pdb=" N CYS U 499 " --> pdb=" O LEU U 731 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'V' and resid 132 through 136 removed outlier: 6.339A pdb=" N VAL V 103 " --> pdb=" O TYR V 133 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER V 135 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU V 105 " --> pdb=" O SER V 135 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE V 10 " --> pdb=" O THR V 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'V' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'V' and resid 297 through 300 removed outlier: 5.851A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'V' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'W' and resid 136 through 139 removed outlier: 6.575A pdb=" N VAL W 17 " --> pdb=" O LEU W 109 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'W' and resid 43 through 47 Processing sheet with id= K, first strand: chain 'W' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'X' and resid 41 through 44 removed outlier: 3.603A pdb=" N GLY X 62 " --> pdb=" O LYS X 44 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'X' and resid 48 through 51 498 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2212 1.29 - 1.44: 3516 1.44 - 1.58: 7658 1.58 - 1.72: 11 1.72 - 1.87: 78 Bond restraints: 13475 Sorted by residual: bond pdb=" C ALA W 136 " pdb=" O ALA W 136 " ideal model delta sigma weight residual 1.234 1.387 -0.152 1.10e-02 8.26e+03 1.92e+02 bond pdb=" C GLY W 11 " pdb=" O GLY W 11 " ideal model delta sigma weight residual 1.236 1.350 -0.114 1.15e-02 7.56e+03 9.89e+01 bond pdb=" C THR W 26 " pdb=" O THR W 26 " ideal model delta sigma weight residual 1.235 1.347 -0.112 1.22e-02 6.72e+03 8.46e+01 bond pdb=" C THR W 175 " pdb=" O THR W 175 " ideal model delta sigma weight residual 1.234 1.318 -0.084 1.23e-02 6.61e+03 4.65e+01 bond pdb=" C TRP G 477 " pdb=" O TRP G 477 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.19e-02 7.06e+03 4.42e+01 ... (remaining 13470 not shown) Histogram of bond angle deviations from ideal: 87.55 - 97.18: 6 97.18 - 106.80: 704 106.80 - 116.43: 8380 116.43 - 126.05: 8840 126.05 - 135.68: 321 Bond angle restraints: 18251 Sorted by residual: angle pdb=" PA ATP W 500 " pdb=" O3A ATP W 500 " pdb=" PB ATP W 500 " ideal model delta sigma weight residual 136.83 114.18 22.65 1.00e+00 1.00e+00 5.13e+02 angle pdb=" PA ATP V 500 " pdb=" O3A ATP V 500 " pdb=" PB ATP V 500 " ideal model delta sigma weight residual 136.83 116.16 20.67 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP W 500 " pdb=" O3B ATP W 500 " pdb=" PG ATP W 500 " ideal model delta sigma weight residual 139.87 119.56 20.31 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP V 500 " pdb=" O3B ATP V 500 " pdb=" PG ATP V 500 " ideal model delta sigma weight residual 139.87 124.18 15.69 1.00e+00 1.00e+00 2.46e+02 angle pdb=" N ILE U 454 " pdb=" CA ILE U 454 " pdb=" CB ILE U 454 " ideal model delta sigma weight residual 111.83 105.01 6.82 6.90e-01 2.10e+00 9.78e+01 ... (remaining 18246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7299 17.45 - 34.89: 722 34.89 - 52.34: 151 52.34 - 69.79: 49 69.79 - 87.23: 13 Dihedral angle restraints: 8234 sinusoidal: 3462 harmonic: 4772 Sorted by residual: dihedral pdb=" CA THR U 184 " pdb=" C THR U 184 " pdb=" N THR U 185 " pdb=" CA THR U 185 " ideal model delta harmonic sigma weight residual -180.00 -139.56 -40.44 0 5.00e+00 4.00e-02 6.54e+01 dihedral pdb=" CA ASP U 207 " pdb=" C ASP U 207 " pdb=" N TYR U 208 " pdb=" CA TYR U 208 " ideal model delta harmonic sigma weight residual -180.00 -146.24 -33.76 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA LEU U 696 " pdb=" C LEU U 696 " pdb=" N LYS U 697 " pdb=" CA LYS U 697 " ideal model delta harmonic sigma weight residual 180.00 -148.05 -31.95 0 5.00e+00 4.00e-02 4.08e+01 ... (remaining 8231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1095 0.074 - 0.147: 646 0.147 - 0.221: 207 0.221 - 0.294: 56 0.294 - 0.368: 6 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CA ILE W 28 " pdb=" N ILE W 28 " pdb=" C ILE W 28 " pdb=" CB ILE W 28 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA ILE V 10 " pdb=" N ILE V 10 " pdb=" C ILE V 10 " pdb=" CB ILE V 10 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB VAL V 129 " pdb=" CA VAL V 129 " pdb=" CG1 VAL V 129 " pdb=" CG2 VAL V 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2007 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR U 490 " -0.098 2.00e-02 2.50e+03 6.14e-02 7.53e+01 pdb=" CG TYR U 490 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR U 490 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR U 490 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR U 490 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR U 490 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR U 490 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR U 490 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 362 " -0.099 2.00e-02 2.50e+03 5.66e-02 6.41e+01 pdb=" CG TYR V 362 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR V 362 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR V 362 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR V 362 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR V 362 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR V 362 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR V 362 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP W 469 " -0.103 2.00e-02 2.50e+03 5.04e-02 6.35e+01 pdb=" CG TRP W 469 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP W 469 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP W 469 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP W 469 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP W 469 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP W 469 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 469 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 469 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP W 469 " -0.015 2.00e-02 2.50e+03 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 17 2.45 - 3.06: 8533 3.06 - 3.68: 18505 3.68 - 4.29: 28962 4.29 - 4.90: 47902 Nonbonded interactions: 103919 Sorted by model distance: nonbonded pdb=" O2G ATP W 500 " pdb="MG MG W 501 " model vdw 1.838 2.170 nonbonded pdb=" O1B ATP W 500 " pdb="MG MG W 501 " model vdw 1.943 2.170 nonbonded pdb=" O2B ATP V 500 " pdb="MG MG V 501 " model vdw 2.036 2.170 nonbonded pdb=" O2G ATP V 500 " pdb="MG MG V 501 " model vdw 2.064 2.170 nonbonded pdb=" OH TYR G 473 " pdb=" OH TYR W 138 " model vdw 2.185 2.440 ... (remaining 103914 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 individual isotropic 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: 0.810 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: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 38.280 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 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 : 0.016 0.152 13475 Z= 1.038 Angle : 2.080 22.655 18251 Z= 1.498 Chirality : 0.099 0.368 2010 Planarity : 0.011 0.061 2336 Dihedral : 15.440 87.233 5138 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.90 % Favored : 94.73 % Rotamer: Outliers : 2.26 % Allowed : 5.56 % Favored : 92.18 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.22 (0.18), residues: 1613 helix: -2.08 (0.16), residues: 702 sheet: -0.25 (0.38), residues: 171 loop : -0.96 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.018 TRP W 469 HIS 0.033 0.007 HIS W 162 PHE 0.070 0.013 PHE W 207 TYR 0.106 0.015 TYR W 450 ARG 0.023 0.003 ARG G 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 294 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 HIS cc_start: 0.6650 (t-90) cc_final: 0.6286 (t70) REVERT: G 479 ASP cc_start: 0.5701 (m-30) cc_final: 0.5402 (t0) REVERT: G 488 MET cc_start: 0.6004 (tpt) cc_final: 0.5753 (tpt) REVERT: G 519 SER cc_start: 0.7649 (t) cc_final: 0.7366 (p) REVERT: G 522 PHE cc_start: 0.6432 (t80) cc_final: 0.6192 (t80) REVERT: U 202 LYS cc_start: 0.7414 (mttt) cc_final: 0.7207 (mptt) REVERT: U 212 ASP cc_start: 0.7353 (m-30) cc_final: 0.6887 (t0) REVERT: U 283 PRO cc_start: 0.8440 (OUTLIER) cc_final: 0.8188 (Cg_exo) REVERT: U 316 GLN cc_start: 0.6451 (mp10) cc_final: 0.6251 (mp10) REVERT: U 338 MET cc_start: 0.7669 (mmt) cc_final: 0.7404 (mmt) REVERT: U 374 ILE cc_start: 0.8001 (mt) cc_final: 0.7604 (tt) REVERT: U 497 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7547 (p) REVERT: U 546 PHE cc_start: 0.7435 (t80) cc_final: 0.7117 (t80) REVERT: U 556 LYS cc_start: 0.6848 (mtmm) cc_final: 0.6512 (mtpp) REVERT: U 576 ASP cc_start: 0.7103 (m-30) cc_final: 0.6613 (p0) REVERT: U 586 ASN cc_start: 0.7323 (t0) cc_final: 0.6990 (t0) REVERT: U 601 PHE cc_start: 0.6483 (t80) cc_final: 0.6208 (t80) REVERT: U 626 LYS cc_start: 0.8055 (mttt) cc_final: 0.7642 (mppt) REVERT: U 631 GLU cc_start: 0.7578 (tt0) cc_final: 0.7255 (pt0) REVERT: U 661 LEU cc_start: 0.7999 (mt) cc_final: 0.7627 (mp) REVERT: U 687 ASP cc_start: 0.7177 (m-30) cc_final: 0.6902 (t0) REVERT: U 690 GLU cc_start: 0.7826 (tt0) cc_final: 0.7216 (pt0) REVERT: U 694 ASN cc_start: 0.4841 (m-40) cc_final: 0.4579 (t0) REVERT: U 713 ASN cc_start: 0.7716 (m-40) cc_final: 0.7418 (m110) REVERT: U 723 MET cc_start: 0.7714 (ttm) cc_final: 0.7309 (ttp) REVERT: U 773 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7958 (tt0) REVERT: V 52 SER cc_start: 0.8695 (p) cc_final: 0.8277 (m) REVERT: V 53 TYR cc_start: 0.7810 (m-80) cc_final: 0.7524 (m-80) REVERT: V 62 ARG cc_start: 0.6617 (ttm-80) cc_final: 0.6302 (ttm110) REVERT: V 83 GLU cc_start: 0.6425 (tt0) cc_final: 0.6198 (tm-30) REVERT: V 241 GLU cc_start: 0.7297 (tt0) cc_final: 0.7085 (tt0) REVERT: V 305 MET cc_start: 0.7907 (mmm) cc_final: 0.7557 (mmm) REVERT: V 355 MET cc_start: 0.7689 (mtm) cc_final: 0.7473 (mtm) REVERT: V 360 GLN cc_start: 0.6659 (tt0) cc_final: 0.5990 (mm110) REVERT: V 364 GLU cc_start: 0.7121 (tt0) cc_final: 0.6534 (mm-30) REVERT: V 375 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: W 13 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6744 (mp0) REVERT: W 33 SER cc_start: 0.7284 (m) cc_final: 0.6863 (p) REVERT: W 59 GLU cc_start: 0.7918 (tt0) cc_final: 0.7662 (tt0) REVERT: W 91 GLN cc_start: 0.6472 (tt0) cc_final: 0.6131 (tp-100) REVERT: W 132 MET cc_start: 0.5781 (mtm) cc_final: 0.5550 (mtp) REVERT: W 196 LYS cc_start: 0.6515 (tttt) cc_final: 0.6269 (mtmm) REVERT: W 219 LYS cc_start: 0.6215 (tttm) cc_final: 0.5971 (ttpt) REVERT: W 298 ASP cc_start: 0.8124 (m-30) cc_final: 0.7890 (p0) REVERT: W 313 LYS cc_start: 0.6270 (tttt) cc_final: 0.6010 (tptt) REVERT: W 436 LYS cc_start: 0.7270 (mttt) cc_final: 0.6959 (pttp) REVERT: W 454 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6492 (tt) REVERT: W 481 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7648 (pm20) REVERT: X 44 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6721 (mmmm) REVERT: X 54 SER cc_start: 0.7738 (t) cc_final: 0.7459 (p) REVERT: X 56 TYR cc_start: 0.6868 (m-80) cc_final: 0.6650 (m-80) outliers start: 33 outliers final: 14 residues processed: 324 average time/residue: 0.2996 time to fit residues: 134.6427 Evaluate side-chains 219 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 451 PRO Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 283 PRO Chi-restraints excluded: chain U residue 497 SER Chi-restraints excluded: chain U residue 553 ILE Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 375 PHE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 142 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 425 MET Chi-restraints excluded: chain W residue 454 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN U 319 GLN U 475 GLN U 660 ASN U 792 ASN U 799 GLN U 862 ASN U 868 HIS V 92 ASN V 115 ASN V 228 GLN W 7 GLN W 53 ASN W 183 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13475 Z= 0.207 Angle : 0.621 17.409 18251 Z= 0.329 Chirality : 0.045 0.151 2010 Planarity : 0.004 0.045 2336 Dihedral : 9.650 68.133 1894 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 2.20 % Allowed : 10.02 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.20), residues: 1613 helix: 0.05 (0.19), residues: 717 sheet: 0.25 (0.36), residues: 211 loop : -0.17 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 340 HIS 0.004 0.001 HIS U 817 PHE 0.017 0.002 PHE U 546 TYR 0.021 0.001 TYR U 596 ARG 0.004 0.000 ARG U 674 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.7461 (t) cc_final: 0.7150 (p) REVERT: U 202 LYS cc_start: 0.7192 (mttt) cc_final: 0.6930 (mptt) REVERT: U 207 ASP cc_start: 0.6796 (t0) cc_final: 0.6022 (t0) REVERT: U 212 ASP cc_start: 0.7119 (m-30) cc_final: 0.6617 (t0) REVERT: U 338 MET cc_start: 0.7691 (mmt) cc_final: 0.7457 (mmt) REVERT: U 374 ILE cc_start: 0.7897 (mt) cc_final: 0.7645 (tt) REVERT: U 576 ASP cc_start: 0.7215 (m-30) cc_final: 0.6623 (p0) REVERT: U 586 ASN cc_start: 0.7143 (t0) cc_final: 0.6818 (t0) REVERT: U 626 LYS cc_start: 0.7836 (mttt) cc_final: 0.7551 (mppt) REVERT: U 631 GLU cc_start: 0.7447 (tt0) cc_final: 0.7124 (pt0) REVERT: U 690 GLU cc_start: 0.7847 (tt0) cc_final: 0.7281 (pt0) REVERT: U 694 ASN cc_start: 0.4974 (m-40) cc_final: 0.4710 (t0) REVERT: U 713 ASN cc_start: 0.6323 (m-40) cc_final: 0.6073 (m110) REVERT: V 62 ARG cc_start: 0.6672 (ttm-80) cc_final: 0.6360 (ttm110) REVERT: V 355 MET cc_start: 0.7468 (mtm) cc_final: 0.7109 (mtm) REVERT: V 364 GLU cc_start: 0.6980 (tt0) cc_final: 0.6397 (mm-30) REVERT: V 375 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: W 33 SER cc_start: 0.7305 (m) cc_final: 0.6849 (p) REVERT: W 91 GLN cc_start: 0.5644 (tt0) cc_final: 0.5400 (tp-100) REVERT: W 182 ARG cc_start: 0.7022 (ptt180) cc_final: 0.6503 (ttp-110) REVERT: W 219 LYS cc_start: 0.6110 (tttm) cc_final: 0.5857 (ttpt) REVERT: W 277 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7444 (tt0) REVERT: W 298 ASP cc_start: 0.8090 (m-30) cc_final: 0.7887 (p0) REVERT: W 313 LYS cc_start: 0.5720 (tttt) cc_final: 0.5426 (tptt) REVERT: W 436 LYS cc_start: 0.7003 (mttt) cc_final: 0.6758 (pttp) REVERT: W 481 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7565 (pm20) REVERT: X 45 ASN cc_start: 0.7754 (m110) cc_final: 0.7416 (t0) REVERT: X 54 SER cc_start: 0.7537 (t) cc_final: 0.7124 (p) REVERT: X 56 TYR cc_start: 0.7003 (m-80) cc_final: 0.6705 (m-80) outliers start: 32 outliers final: 20 residues processed: 226 average time/residue: 0.2924 time to fit residues: 95.3801 Evaluate side-chains 193 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 553 ILE Chi-restraints excluded: chain U residue 555 SER Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 184 ASP Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 375 PHE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 425 MET Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 chunk 159 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 468 HIS U 194 GLN U 713 ASN ** U 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13475 Z= 0.206 Angle : 0.534 9.539 18251 Z= 0.284 Chirality : 0.043 0.162 2010 Planarity : 0.004 0.042 2336 Dihedral : 8.658 67.391 1873 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.40 % Rotamer: Outliers : 2.54 % Allowed : 11.67 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.21), residues: 1613 helix: 0.63 (0.20), residues: 717 sheet: 0.51 (0.36), residues: 216 loop : -0.10 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 340 HIS 0.004 0.001 HIS W 162 PHE 0.014 0.001 PHE W 207 TYR 0.015 0.001 TYR W 450 ARG 0.006 0.000 ARG X 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 519 SER cc_start: 0.7424 (t) cc_final: 0.7120 (p) REVERT: U 183 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7036 (mm-30) REVERT: U 202 LYS cc_start: 0.7187 (mttt) cc_final: 0.6947 (mptt) REVERT: U 207 ASP cc_start: 0.6828 (t0) cc_final: 0.6049 (t0) REVERT: U 212 ASP cc_start: 0.7045 (m-30) cc_final: 0.6510 (t0) REVERT: U 318 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8058 (pp20) REVERT: U 338 MET cc_start: 0.7746 (mmt) cc_final: 0.7524 (mmt) REVERT: U 374 ILE cc_start: 0.7861 (mt) cc_final: 0.7605 (tt) REVERT: U 576 ASP cc_start: 0.7214 (m-30) cc_final: 0.6609 (p0) REVERT: U 586 ASN cc_start: 0.7106 (t0) cc_final: 0.6805 (t0) REVERT: U 626 LYS cc_start: 0.7865 (mttt) cc_final: 0.7513 (mppt) REVERT: U 631 GLU cc_start: 0.7518 (tt0) cc_final: 0.7164 (pt0) REVERT: U 690 GLU cc_start: 0.7757 (tt0) cc_final: 0.7228 (pt0) REVERT: V 62 ARG cc_start: 0.6580 (ttm-80) cc_final: 0.6275 (ttm110) REVERT: V 355 MET cc_start: 0.7446 (mtm) cc_final: 0.6985 (mtm) REVERT: V 364 GLU cc_start: 0.7046 (tt0) cc_final: 0.6476 (mm-30) REVERT: V 375 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: W 33 SER cc_start: 0.7223 (m) cc_final: 0.6731 (p) REVERT: W 91 GLN cc_start: 0.5596 (tt0) cc_final: 0.5254 (tp-100) REVERT: W 219 LYS cc_start: 0.6218 (tttm) cc_final: 0.5981 (ttpt) REVERT: W 277 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7494 (tt0) REVERT: W 298 ASP cc_start: 0.8251 (m-30) cc_final: 0.8023 (p0) REVERT: W 313 LYS cc_start: 0.5653 (tttt) cc_final: 0.5399 (tptt) REVERT: W 436 LYS cc_start: 0.7087 (mttt) cc_final: 0.6869 (pttp) REVERT: W 481 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7539 (pm20) REVERT: X 45 ASN cc_start: 0.7946 (m110) cc_final: 0.7567 (t0) REVERT: X 54 SER cc_start: 0.7743 (t) cc_final: 0.7338 (p) REVERT: X 56 TYR cc_start: 0.6977 (m-80) cc_final: 0.6649 (m-80) outliers start: 37 outliers final: 26 residues processed: 206 average time/residue: 0.2632 time to fit residues: 78.1379 Evaluate side-chains 194 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 553 ILE Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 184 ASP Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 375 PHE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 174 MET Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 446 ILE Chi-restraints excluded: chain W residue 462 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 98 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 156 optimal weight: 0.0470 chunk 77 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 709 GLN U 713 ASN V 228 GLN V 372 HIS W 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13475 Z= 0.134 Angle : 0.468 6.711 18251 Z= 0.248 Chirality : 0.042 0.175 2010 Planarity : 0.004 0.035 2336 Dihedral : 7.714 69.871 1868 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.77 % Rotamer: Outliers : 2.13 % Allowed : 12.42 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.21), residues: 1613 helix: 1.11 (0.20), residues: 713 sheet: 0.86 (0.38), residues: 194 loop : 0.18 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 340 HIS 0.003 0.001 HIS W 162 PHE 0.009 0.001 PHE U 223 TYR 0.012 0.001 TYR U 596 ARG 0.005 0.000 ARG W 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 183 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6992 (mm-30) REVERT: U 202 LYS cc_start: 0.7133 (mttt) cc_final: 0.6852 (mptt) REVERT: U 207 ASP cc_start: 0.6713 (t0) cc_final: 0.5975 (t0) REVERT: U 212 ASP cc_start: 0.7016 (m-30) cc_final: 0.6484 (t0) REVERT: U 318 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8039 (pp20) REVERT: U 338 MET cc_start: 0.7778 (mmt) cc_final: 0.7550 (mmt) REVERT: U 374 ILE cc_start: 0.7908 (mt) cc_final: 0.7691 (tt) REVERT: U 576 ASP cc_start: 0.7097 (m-30) cc_final: 0.6459 (p0) REVERT: U 586 ASN cc_start: 0.7195 (t0) cc_final: 0.6915 (t0) REVERT: U 626 LYS cc_start: 0.7861 (mttt) cc_final: 0.7515 (mppt) REVERT: U 631 GLU cc_start: 0.7574 (tt0) cc_final: 0.7101 (pt0) REVERT: U 687 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5787 (m-30) REVERT: U 690 GLU cc_start: 0.7765 (tt0) cc_final: 0.7288 (pt0) REVERT: V 34 ILE cc_start: 0.8130 (mt) cc_final: 0.7885 (pt) REVERT: V 62 ARG cc_start: 0.6628 (ttm-80) cc_final: 0.6340 (ttm110) REVERT: V 68 ARG cc_start: 0.5945 (mtp180) cc_final: 0.5537 (mtt-85) REVERT: V 355 MET cc_start: 0.7292 (mtm) cc_final: 0.6837 (mtm) REVERT: V 364 GLU cc_start: 0.7026 (tt0) cc_final: 0.6478 (mm-30) REVERT: W 33 SER cc_start: 0.7144 (m) cc_final: 0.6646 (p) REVERT: W 91 GLN cc_start: 0.5473 (tt0) cc_final: 0.5141 (tp-100) REVERT: W 182 ARG cc_start: 0.6803 (ptt180) cc_final: 0.6311 (ttp-110) REVERT: W 277 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7520 (tt0) REVERT: W 313 LYS cc_start: 0.5648 (tttt) cc_final: 0.5396 (tptt) REVERT: W 436 LYS cc_start: 0.6880 (mttt) cc_final: 0.6668 (pttp) REVERT: W 481 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7550 (pm20) REVERT: X 45 ASN cc_start: 0.7766 (m110) cc_final: 0.7446 (t0) REVERT: X 54 SER cc_start: 0.7763 (t) cc_final: 0.7357 (p) REVERT: X 56 TYR cc_start: 0.6848 (m-80) cc_final: 0.6637 (m-80) REVERT: X 64 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7344 (tt) outliers start: 31 outliers final: 17 residues processed: 213 average time/residue: 0.2700 time to fit residues: 83.0921 Evaluate side-chains 188 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 687 ASP Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 184 ASP Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 0.0970 chunk 140 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 468 HIS G 541 ASN V 228 GLN V 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13475 Z= 0.210 Angle : 0.485 8.484 18251 Z= 0.255 Chirality : 0.043 0.176 2010 Planarity : 0.004 0.038 2336 Dihedral : 7.446 70.516 1862 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.88 % Allowed : 12.83 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.21), residues: 1613 helix: 1.07 (0.20), residues: 717 sheet: 0.84 (0.38), residues: 202 loop : 0.07 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 356 HIS 0.006 0.001 HIS G 468 PHE 0.013 0.001 PHE W 207 TYR 0.015 0.001 TYR W 450 ARG 0.005 0.000 ARG G 548 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7707 (tt0) REVERT: U 183 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7021 (mm-30) REVERT: U 202 LYS cc_start: 0.7082 (mttt) cc_final: 0.6833 (mptt) REVERT: U 207 ASP cc_start: 0.7001 (t0) cc_final: 0.6217 (t0) REVERT: U 212 ASP cc_start: 0.7018 (m-30) cc_final: 0.6472 (t0) REVERT: U 318 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8043 (pp20) REVERT: U 374 ILE cc_start: 0.7923 (mt) cc_final: 0.7593 (tt) REVERT: U 576 ASP cc_start: 0.7186 (m-30) cc_final: 0.6506 (p0) REVERT: U 586 ASN cc_start: 0.6913 (t0) cc_final: 0.6658 (t0) REVERT: U 598 PHE cc_start: 0.6701 (p90) cc_final: 0.6490 (p90) REVERT: U 626 LYS cc_start: 0.7812 (mttt) cc_final: 0.7494 (mppt) REVERT: U 631 GLU cc_start: 0.7498 (tt0) cc_final: 0.7017 (pt0) REVERT: U 687 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5771 (m-30) REVERT: U 690 GLU cc_start: 0.7717 (tt0) cc_final: 0.7225 (pt0) REVERT: V 34 ILE cc_start: 0.8171 (mt) cc_final: 0.7908 (pt) REVERT: V 62 ARG cc_start: 0.6621 (ttm-80) cc_final: 0.6372 (ttm110) REVERT: V 82 MET cc_start: 0.6866 (tpt) cc_final: 0.6374 (tpt) REVERT: V 355 MET cc_start: 0.7299 (mtm) cc_final: 0.6794 (mtm) REVERT: V 364 GLU cc_start: 0.7069 (tt0) cc_final: 0.6525 (mm-30) REVERT: W 33 SER cc_start: 0.7132 (m) cc_final: 0.6641 (p) REVERT: W 91 GLN cc_start: 0.5579 (tt0) cc_final: 0.5279 (tp-100) REVERT: W 182 ARG cc_start: 0.6883 (ptt180) cc_final: 0.6316 (ttp-110) REVERT: W 277 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7615 (tt0) REVERT: W 436 LYS cc_start: 0.6889 (mttt) cc_final: 0.6684 (pttp) REVERT: W 481 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7557 (pm20) REVERT: X 45 ASN cc_start: 0.7780 (m110) cc_final: 0.7483 (t0) REVERT: X 54 SER cc_start: 0.7792 (t) cc_final: 0.7391 (p) REVERT: X 64 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7345 (tt) outliers start: 42 outliers final: 31 residues processed: 202 average time/residue: 0.2663 time to fit residues: 78.7518 Evaluate side-chains 202 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 687 ASP Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 411 THR Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 709 GLN U 713 ASN V 101 HIS V 228 GLN V 372 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13475 Z= 0.162 Angle : 0.460 6.788 18251 Z= 0.241 Chirality : 0.042 0.175 2010 Planarity : 0.004 0.036 2336 Dihedral : 7.233 70.137 1862 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.23 % Favored : 97.64 % Rotamer: Outliers : 2.54 % Allowed : 13.38 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.21), residues: 1613 helix: 1.12 (0.20), residues: 721 sheet: 0.71 (0.37), residues: 209 loop : 0.08 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 340 HIS 0.003 0.001 HIS W 162 PHE 0.013 0.001 PHE U 766 TYR 0.012 0.001 TYR U 596 ARG 0.004 0.000 ARG G 548 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7699 (tt0) REVERT: U 183 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6987 (mm-30) REVERT: U 202 LYS cc_start: 0.7070 (mttt) cc_final: 0.6821 (mptt) REVERT: U 207 ASP cc_start: 0.6932 (t0) cc_final: 0.6189 (t0) REVERT: U 212 ASP cc_start: 0.7179 (m-30) cc_final: 0.6593 (t0) REVERT: U 374 ILE cc_start: 0.7932 (mt) cc_final: 0.7604 (tt) REVERT: U 576 ASP cc_start: 0.7226 (m-30) cc_final: 0.6542 (p0) REVERT: U 586 ASN cc_start: 0.6925 (t0) cc_final: 0.6656 (t0) REVERT: U 598 PHE cc_start: 0.6757 (p90) cc_final: 0.6552 (p90) REVERT: U 626 LYS cc_start: 0.7817 (mttt) cc_final: 0.7494 (mppt) REVERT: U 631 GLU cc_start: 0.7581 (tt0) cc_final: 0.7114 (pt0) REVERT: U 687 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5712 (m-30) REVERT: U 690 GLU cc_start: 0.7769 (tt0) cc_final: 0.7276 (pt0) REVERT: V 34 ILE cc_start: 0.8186 (mt) cc_final: 0.7952 (pt) REVERT: V 62 ARG cc_start: 0.6688 (ttm-80) cc_final: 0.6484 (ttm110) REVERT: V 355 MET cc_start: 0.7407 (mtm) cc_final: 0.6899 (mtm) REVERT: V 364 GLU cc_start: 0.7056 (tt0) cc_final: 0.6517 (mm-30) REVERT: W 91 GLN cc_start: 0.5520 (tt0) cc_final: 0.5229 (tp-100) REVERT: W 182 ARG cc_start: 0.6898 (ptt180) cc_final: 0.6347 (ttp-110) REVERT: W 448 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6235 (mtm180) REVERT: W 481 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7536 (pm20) REVERT: W 489 ARG cc_start: 0.5900 (ttm-80) cc_final: 0.5580 (ttm-80) REVERT: X 45 ASN cc_start: 0.7717 (m110) cc_final: 0.7429 (t0) REVERT: X 54 SER cc_start: 0.7618 (t) cc_final: 0.7217 (p) REVERT: X 57 LYS cc_start: 0.7315 (mtmt) cc_final: 0.6967 (ttmm) REVERT: X 64 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7323 (tt) REVERT: X 69 ARG cc_start: 0.6240 (ttp80) cc_final: 0.6023 (ttp80) outliers start: 37 outliers final: 30 residues processed: 198 average time/residue: 0.2772 time to fit residues: 78.8572 Evaluate side-chains 203 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 687 ASP Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 448 ARG Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 131 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 709 GLN U 713 ASN V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13475 Z= 0.167 Angle : 0.456 6.059 18251 Z= 0.238 Chirality : 0.042 0.178 2010 Planarity : 0.004 0.036 2336 Dihedral : 7.063 69.836 1862 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.17 % Favored : 97.71 % Rotamer: Outliers : 2.81 % Allowed : 13.52 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1613 helix: 1.16 (0.20), residues: 721 sheet: 0.69 (0.37), residues: 209 loop : 0.12 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 340 HIS 0.004 0.001 HIS W 162 PHE 0.015 0.001 PHE U 378 TYR 0.018 0.001 TYR W 319 ARG 0.002 0.000 ARG V 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7669 (tt0) REVERT: U 183 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6958 (mm-30) REVERT: U 202 LYS cc_start: 0.7082 (mttt) cc_final: 0.6841 (mptt) REVERT: U 207 ASP cc_start: 0.6908 (t0) cc_final: 0.6197 (t0) REVERT: U 318 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8038 (pp20) REVERT: U 374 ILE cc_start: 0.8069 (mt) cc_final: 0.7741 (tt) REVERT: U 576 ASP cc_start: 0.7207 (m-30) cc_final: 0.6521 (p0) REVERT: U 586 ASN cc_start: 0.6933 (t0) cc_final: 0.6660 (t0) REVERT: U 626 LYS cc_start: 0.7789 (mttt) cc_final: 0.7474 (mppt) REVERT: U 631 GLU cc_start: 0.7430 (tt0) cc_final: 0.6907 (pt0) REVERT: U 687 ASP cc_start: 0.6142 (OUTLIER) cc_final: 0.5714 (m-30) REVERT: U 690 GLU cc_start: 0.7803 (tt0) cc_final: 0.7286 (pt0) REVERT: V 34 ILE cc_start: 0.8209 (mt) cc_final: 0.7986 (pt) REVERT: V 82 MET cc_start: 0.6887 (tpt) cc_final: 0.6355 (tpt) REVERT: V 355 MET cc_start: 0.7287 (mtm) cc_final: 0.6774 (mtm) REVERT: V 360 GLN cc_start: 0.6222 (tt0) cc_final: 0.5627 (mm110) REVERT: V 364 GLU cc_start: 0.7067 (tt0) cc_final: 0.6550 (mm-30) REVERT: W 91 GLN cc_start: 0.5515 (tt0) cc_final: 0.5231 (tp-100) REVERT: W 182 ARG cc_start: 0.6908 (ptt180) cc_final: 0.6351 (ttp-110) REVERT: W 448 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6214 (mtm180) REVERT: W 481 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7510 (pm20) REVERT: X 45 ASN cc_start: 0.7787 (m110) cc_final: 0.7522 (t0) REVERT: X 54 SER cc_start: 0.7515 (t) cc_final: 0.7109 (p) REVERT: X 57 LYS cc_start: 0.7305 (mtmt) cc_final: 0.6934 (ttmm) REVERT: X 64 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7387 (mt) outliers start: 41 outliers final: 37 residues processed: 197 average time/residue: 0.2571 time to fit residues: 73.8956 Evaluate side-chains 208 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 687 ASP Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 733 VAL Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 841 ILE Chi-restraints excluded: chain U residue 868 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 110 MET Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 177 SER Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 448 ARG Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 99 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 709 GLN U 713 ASN V 228 GLN V 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13475 Z= 0.158 Angle : 0.451 5.516 18251 Z= 0.235 Chirality : 0.041 0.181 2010 Planarity : 0.004 0.036 2336 Dihedral : 6.900 69.862 1862 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.54 % Allowed : 14.07 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.21), residues: 1613 helix: 1.24 (0.20), residues: 721 sheet: 0.71 (0.38), residues: 209 loop : 0.18 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 340 HIS 0.003 0.000 HIS W 162 PHE 0.022 0.001 PHE U 598 TYR 0.012 0.001 TYR U 596 ARG 0.009 0.000 ARG X 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7766 (tt0) REVERT: U 183 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6971 (mm-30) REVERT: U 202 LYS cc_start: 0.7071 (mttt) cc_final: 0.6833 (mptt) REVERT: U 207 ASP cc_start: 0.6885 (t0) cc_final: 0.6192 (t0) REVERT: U 374 ILE cc_start: 0.8076 (mt) cc_final: 0.7751 (tt) REVERT: U 576 ASP cc_start: 0.7198 (m-30) cc_final: 0.6506 (p0) REVERT: U 586 ASN cc_start: 0.6918 (t0) cc_final: 0.6655 (t0) REVERT: U 626 LYS cc_start: 0.7778 (mttt) cc_final: 0.7457 (mppt) REVERT: U 631 GLU cc_start: 0.7430 (tt0) cc_final: 0.6912 (pt0) REVERT: U 687 ASP cc_start: 0.6180 (OUTLIER) cc_final: 0.5807 (m-30) REVERT: U 690 GLU cc_start: 0.7830 (tt0) cc_final: 0.7355 (pt0) REVERT: V 34 ILE cc_start: 0.8203 (mt) cc_final: 0.7998 (pt) REVERT: V 68 ARG cc_start: 0.6102 (mtp180) cc_final: 0.5742 (mtt-85) REVERT: V 82 MET cc_start: 0.6853 (tpt) cc_final: 0.6430 (tpt) REVERT: V 355 MET cc_start: 0.7286 (mtm) cc_final: 0.6774 (mtm) REVERT: V 360 GLN cc_start: 0.6204 (tt0) cc_final: 0.5615 (mm110) REVERT: V 364 GLU cc_start: 0.7070 (tt0) cc_final: 0.6562 (mm-30) REVERT: W 91 GLN cc_start: 0.5381 (tt0) cc_final: 0.5115 (tp-100) REVERT: W 174 MET cc_start: 0.5942 (mtm) cc_final: 0.5572 (mtm) REVERT: W 182 ARG cc_start: 0.6914 (ptt180) cc_final: 0.6352 (ttp-110) REVERT: W 448 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6261 (mtm180) REVERT: W 481 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7499 (pm20) REVERT: X 45 ASN cc_start: 0.7792 (m110) cc_final: 0.7546 (t0) REVERT: X 57 LYS cc_start: 0.7303 (mtmt) cc_final: 0.6902 (ttmm) REVERT: X 64 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7299 (mt) outliers start: 37 outliers final: 31 residues processed: 196 average time/residue: 0.2592 time to fit residues: 74.8779 Evaluate side-chains 202 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 364 ILE Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 687 ASP Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 823 HIS Chi-restraints excluded: chain U residue 868 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 448 ARG Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 709 GLN U 713 ASN U 799 GLN V 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13475 Z= 0.166 Angle : 0.447 5.379 18251 Z= 0.233 Chirality : 0.042 0.181 2010 Planarity : 0.004 0.036 2336 Dihedral : 6.813 69.344 1862 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Rotamer: Outliers : 2.81 % Allowed : 13.80 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.21), residues: 1613 helix: 1.26 (0.20), residues: 721 sheet: 0.70 (0.38), residues: 209 loop : 0.19 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 551 HIS 0.004 0.001 HIS W 162 PHE 0.018 0.001 PHE U 378 TYR 0.012 0.001 TYR U 596 ARG 0.007 0.000 ARG X 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7767 (tt0) REVERT: U 183 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7000 (mm-30) REVERT: U 202 LYS cc_start: 0.7062 (mttt) cc_final: 0.6761 (mptt) REVERT: U 207 ASP cc_start: 0.6909 (t0) cc_final: 0.6230 (t0) REVERT: U 374 ILE cc_start: 0.8068 (mt) cc_final: 0.7760 (tt) REVERT: U 576 ASP cc_start: 0.7201 (m-30) cc_final: 0.6510 (p0) REVERT: U 586 ASN cc_start: 0.6933 (t0) cc_final: 0.6677 (t0) REVERT: U 626 LYS cc_start: 0.7803 (mttt) cc_final: 0.7505 (mppt) REVERT: U 631 GLU cc_start: 0.7407 (tt0) cc_final: 0.6890 (pt0) REVERT: U 687 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5739 (m-30) REVERT: U 690 GLU cc_start: 0.7749 (tt0) cc_final: 0.7251 (pt0) REVERT: V 34 ILE cc_start: 0.8208 (mt) cc_final: 0.8001 (pt) REVERT: V 68 ARG cc_start: 0.6098 (mtp180) cc_final: 0.5743 (mtt-85) REVERT: V 82 MET cc_start: 0.6904 (tpt) cc_final: 0.6413 (tpt) REVERT: V 355 MET cc_start: 0.7250 (mtm) cc_final: 0.6714 (mtm) REVERT: V 360 GLN cc_start: 0.6204 (tt0) cc_final: 0.5618 (mm110) REVERT: V 364 GLU cc_start: 0.7063 (tt0) cc_final: 0.6552 (mm-30) REVERT: W 75 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6800 (mp) REVERT: W 91 GLN cc_start: 0.5381 (tt0) cc_final: 0.5119 (tp-100) REVERT: W 182 ARG cc_start: 0.6915 (ptt180) cc_final: 0.6352 (ttp-110) REVERT: W 448 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6237 (mtm180) REVERT: W 481 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7499 (pm20) REVERT: X 45 ASN cc_start: 0.7802 (m110) cc_final: 0.7560 (t0) REVERT: X 57 LYS cc_start: 0.7303 (mtmt) cc_final: 0.6899 (ttmm) REVERT: X 64 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7308 (mt) outliers start: 41 outliers final: 33 residues processed: 198 average time/residue: 0.2507 time to fit residues: 73.3556 Evaluate side-chains 206 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 687 ASP Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 868 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 110 MET Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 211 GLN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 448 ARG Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 128 optimal weight: 0.0020 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 709 GLN U 713 ASN V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13475 Z= 0.145 Angle : 0.440 5.609 18251 Z= 0.229 Chirality : 0.041 0.181 2010 Planarity : 0.004 0.035 2336 Dihedral : 6.653 69.206 1862 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 2.47 % Allowed : 14.28 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.21), residues: 1613 helix: 1.36 (0.20), residues: 719 sheet: 0.70 (0.38), residues: 209 loop : 0.26 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 340 HIS 0.003 0.000 HIS W 162 PHE 0.018 0.001 PHE U 378 TYR 0.016 0.001 TYR W 319 ARG 0.007 0.000 ARG X 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 549 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7762 (tt0) REVERT: U 183 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6939 (mm-30) REVERT: U 202 LYS cc_start: 0.7053 (mttt) cc_final: 0.6755 (mptt) REVERT: U 207 ASP cc_start: 0.6863 (t0) cc_final: 0.6208 (t0) REVERT: U 374 ILE cc_start: 0.8036 (mt) cc_final: 0.7729 (tt) REVERT: U 576 ASP cc_start: 0.7202 (m-30) cc_final: 0.6710 (p0) REVERT: U 586 ASN cc_start: 0.6949 (t0) cc_final: 0.6707 (t0) REVERT: U 599 LYS cc_start: 0.7002 (tptt) cc_final: 0.6761 (tptp) REVERT: U 626 LYS cc_start: 0.7630 (mttt) cc_final: 0.7353 (mppt) REVERT: U 631 GLU cc_start: 0.7402 (tt0) cc_final: 0.6889 (pt0) REVERT: U 687 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5718 (m-30) REVERT: U 690 GLU cc_start: 0.7844 (tt0) cc_final: 0.7272 (pt0) REVERT: V 82 MET cc_start: 0.6782 (tpt) cc_final: 0.6393 (tpt) REVERT: V 355 MET cc_start: 0.7238 (mtm) cc_final: 0.6711 (mtm) REVERT: V 360 GLN cc_start: 0.6222 (tt0) cc_final: 0.5641 (mm110) REVERT: V 364 GLU cc_start: 0.7082 (tt0) cc_final: 0.6610 (mm-30) REVERT: W 91 GLN cc_start: 0.5460 (tt0) cc_final: 0.5195 (tp-100) REVERT: W 182 ARG cc_start: 0.6909 (ptt180) cc_final: 0.6380 (ttp-110) REVERT: W 448 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6255 (mtm180) REVERT: W 481 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7497 (pm20) REVERT: X 45 ASN cc_start: 0.7786 (m110) cc_final: 0.7557 (t0) REVERT: X 57 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6900 (ttmm) REVERT: X 64 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7310 (mt) outliers start: 36 outliers final: 31 residues processed: 201 average time/residue: 0.2715 time to fit residues: 81.1352 Evaluate side-chains 201 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain U residue 198 LEU Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 290 VAL Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 616 ILE Chi-restraints excluded: chain U residue 656 SER Chi-restraints excluded: chain U residue 687 ASP Chi-restraints excluded: chain U residue 711 ILE Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 737 SER Chi-restraints excluded: chain U residue 868 HIS Chi-restraints excluded: chain U residue 870 SER Chi-restraints excluded: chain V residue 110 MET Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain V residue 299 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 183 ASN Chi-restraints excluded: chain W residue 211 GLN Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 256 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 421 SER Chi-restraints excluded: chain W residue 448 ARG Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 709 GLN U 713 ASN V 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.150375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114167 restraints weight = 16679.057| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.21 r_work: 0.3128 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13475 Z= 0.162 Angle : 0.446 5.392 18251 Z= 0.232 Chirality : 0.041 0.183 2010 Planarity : 0.004 0.035 2336 Dihedral : 6.604 68.173 1862 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.89 % Rotamer: Outliers : 2.20 % Allowed : 14.48 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.21), residues: 1613 helix: 1.31 (0.20), residues: 724 sheet: 0.64 (0.38), residues: 209 loop : 0.20 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 340 HIS 0.003 0.000 HIS W 162 PHE 0.018 0.001 PHE U 378 TYR 0.020 0.001 TYR W 319 ARG 0.007 0.000 ARG X 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3093.50 seconds wall clock time: 56 minutes 51.64 seconds (3411.64 seconds total)