Starting phenix.real_space_refine on Thu Feb 15 14:54:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2024/8a5o_15179_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2024/8a5o_15179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2024/8a5o_15179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2024/8a5o_15179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2024/8a5o_15179_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2024/8a5o_15179_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 50 5.16 5 C 7968 2.51 5 N 2128 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 482": "NH1" <-> "NH2" Residue "G ASP 527": "OD1" <-> "OD2" Residue "G ARG 533": "NH1" <-> "NH2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G ASP 552": "OD1" <-> "OD2" Residue "U ASP 264": "OD1" <-> "OD2" Residue "U ASP 303": "OD1" <-> "OD2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U GLU 322": "OE1" <-> "OE2" Residue "U PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 331": "OE1" <-> "OE2" Residue "U PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 380": "OD1" <-> "OD2" Residue "U ASP 394": "OD1" <-> "OD2" Residue "U PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 545": "OD1" <-> "OD2" Residue "U ASP 554": "OD1" <-> "OD2" 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 GLU 636": "OE1" <-> "OE2" Residue "U GLU 658": "OE1" <-> "OE2" Residue "U ASP 668": "OD1" <-> "OD2" Residue "U PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 789": "OE1" <-> "OE2" Residue "U GLU 809": "OE1" <-> "OE2" Residue "U GLU 810": "OE1" <-> "OE2" Residue "U GLU 816": "OE1" <-> "OE2" Residue "U ARG 834": "NH1" <-> "NH2" Residue "U GLU 856": "OE1" <-> "OE2" Residue "U ARG 871": "NH1" <-> "NH2" Residue "V PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "V ARG 95": "NH1" <-> "NH2" Residue "V GLU 107": "OE1" <-> "OE2" 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 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 275": "OD1" <-> "OD2" Residue "V GLU 292": "OE1" <-> "OE2" Residue "V TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 12": "OD1" <-> "OD2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "W PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 84": "OD1" <-> "OD2" Residue "W GLU 88": "OE1" <-> "OE2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 112": "OE1" <-> "OE2" Residue "W GLU 126": "OE1" <-> "OE2" Residue "W PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 241": "OE1" <-> "OE2" Residue "W ARG 268": "NH1" <-> "NH2" Residue "W GLU 277": "OE1" <-> "OE2" Residue "W PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 281": "OD1" <-> "OD2" Residue "W GLU 283": "OE1" <-> "OE2" Residue "W GLU 291": "OE1" <-> "OE2" Residue "W GLU 381": "OE1" <-> "OE2" 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 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 12571 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 882 Classifications: {'peptide': 103} Link IDs: {'TRANS': 102} Chain: "U" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5060 Classifications: {'peptide': 626} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 594} Chain: "V" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2824 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "W" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3422 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain breaks: 1 Chain: "X" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.72, per 1000 atoms: 0.53 Number of scatterers: 12571 At special positions: 0 Unit cell: (98.487, 135.552, 137.67, 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 50 16.00 P 9 15.00 Mg 3 11.99 O 2413 8.00 N 2128 7.00 C 7968 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: 4.53 Conformation dependent library (CDL) restraints added in 2.3 seconds 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 14 sheets defined 46.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'G' and resid 459 through 482 Processing helix chain 'G' and resid 484 through 518 removed outlier: 3.807A pdb=" N GLN G 518 " --> pdb=" O ALA G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 558 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 304 through 306 No H-bonds generated for 'chain 'U' and resid 304 through 306' Processing helix chain 'U' and resid 321 through 340 Processing helix chain 'U' and resid 349 through 359 removed outlier: 3.540A pdb=" N PHE U 356 " --> pdb=" O GLN U 352 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN U 359 " --> pdb=" O SER U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 386 through 390 Processing helix chain 'U' and resid 418 through 433 Processing helix chain 'U' and resid 442 through 447 removed outlier: 3.712A pdb=" N PHE U 445 " --> pdb=" O PRO U 442 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASN U 446 " --> pdb=" O THR U 443 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 472 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 532 through 544 Processing helix chain 'U' and resid 556 through 569 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: 3.587A pdb=" N LEU U 606 " --> pdb=" O GLU U 603 " (cutoff:3.500A) removed outlier: 4.866A 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 619 Processing helix chain 'U' and resid 628 through 633 Processing helix chain 'U' and resid 651 through 658 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: 5.734A pdb=" N HIS U 679 " --> pdb=" O ILE U 675 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN U 680 " --> pdb=" O LEU U 676 " (cutoff:3.500A) Processing helix chain 'U' and resid 703 through 715 Processing helix chain 'U' and resid 720 through 727 removed outlier: 3.711A pdb=" N ASN U 724 " --> pdb=" O THR U 721 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE U 726 " --> pdb=" O MET U 723 " (cutoff:3.500A) removed outlier: 3.610A 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 756 through 759 No H-bonds generated for 'chain 'U' and resid 756 through 759' Processing helix chain 'U' and resid 763 through 780 Processing helix chain 'U' and resid 789 through 817 removed outlier: 4.187A pdb=" N HIS U 817 " --> pdb=" O GLN U 813 " (cutoff:3.500A) Processing helix chain 'U' and resid 833 through 835 No H-bonds generated for 'chain 'U' and resid 833 through 835' Processing helix chain 'U' and resid 841 through 851 removed outlier: 3.587A pdb=" N GLN U 851 " --> pdb=" O SER U 847 " (cutoff:3.500A) Processing helix chain 'U' and resid 853 through 857 Processing helix chain 'U' and resid 862 through 874 removed outlier: 8.283A pdb=" N SER U 870 " --> pdb=" O ASP U 866 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ARG U 871 " --> pdb=" O VAL U 867 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE U 872 " --> pdb=" O HIS U 868 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU U 873 " --> pdb=" O GLY U 869 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN U 874 " --> pdb=" O SER U 870 " (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: 3.866A 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 125 Processing helix chain 'V' and resid 137 through 145 removed outlier: 3.893A 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 195 Processing helix chain 'V' and resid 203 through 216 removed outlier: 3.629A pdb=" N ILE V 208 " --> pdb=" O ALA V 204 " (cutoff:3.500A) removed outlier: 3.850A 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 234 through 236 No H-bonds generated for 'chain 'V' and resid 234 through 236' Processing helix chain 'V' and resid 252 through 261 removed outlier: 3.536A pdb=" N ARG V 256 " --> pdb=" O GLU V 253 " (cutoff:3.500A) removed outlier: 4.562A 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 282 Processing helix chain 'V' and resid 287 through 296 removed outlier: 3.531A pdb=" N ARG V 290 " --> pdb=" O VAL V 287 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS V 291 " --> pdb=" O ASP V 288 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR V 294 " --> pdb=" O LYS V 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY V 295 " --> pdb=" O GLU V 292 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 305 Processing helix chain 'V' and resid 309 through 320 removed outlier: 3.513A pdb=" N LEU V 320 " --> pdb=" O GLU V 316 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 348 removed outlier: 5.567A pdb=" N VAL V 339 " --> pdb=" O LYS V 336 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY V 342 " --> pdb=" O VAL V 339 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE V 345 " --> pdb=" O GLY V 342 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA V 347 " --> pdb=" O SER V 344 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 352 No H-bonds generated for 'chain 'V' and resid 350 through 352' Processing helix chain 'V' and resid 359 through 365 Processing helix chain 'V' and resid 367 through 373 removed outlier: 3.862A pdb=" N LYS V 373 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 96 Processing helix chain 'W' and resid 118 through 129 removed outlier: 3.602A pdb=" N LEU W 125 " --> pdb=" O ARG W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 150 removed outlier: 3.542A pdb=" N PHE W 148 " --> pdb=" O THR W 144 " (cutoff:3.500A) Processing helix chain 'W' and resid 187 through 198 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 255 through 264 removed outlier: 5.257A pdb=" N THR W 260 " --> pdb=" O GLU W 256 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU W 261 " --> pdb=" O GLU W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 282 through 292 removed outlier: 4.059A pdb=" N ALA W 289 " --> pdb=" O ARG W 285 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU W 292 " --> pdb=" O PHE W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 394 Processing helix chain 'W' and resid 398 through 407 removed outlier: 3.562A pdb=" N ARG W 401 " --> pdb=" O VAL W 398 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA W 402 " --> pdb=" O ASP W 399 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS W 406 " --> pdb=" O THR W 403 " (cutoff:3.500A) Processing helix chain 'W' and resid 413 through 416 removed outlier: 3.968A pdb=" N SER W 416 " --> pdb=" O GLY W 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 413 through 416' Processing helix chain 'W' and resid 420 through 431 Processing helix chain 'W' and resid 447 through 461 removed outlier: 6.778A pdb=" N SER W 452 " --> pdb=" O ARG W 448 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TRP W 453 " --> pdb=" O GLN W 449 " (cutoff:3.500A) Processing helix chain 'W' and resid 463 through 468 removed outlier: 4.511A pdb=" N GLN W 467 " --> pdb=" O THR W 464 " (cutoff:3.500A) Processing helix chain 'W' and resid 472 through 478 Processing helix chain 'W' and resid 480 through 486 removed outlier: 3.846A pdb=" N ASN W 485 " --> pdb=" O GLU W 481 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'U' and resid 289 through 292 removed outlier: 6.372A pdb=" N LYS U 449 " --> pdb=" O ILE U 269 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE U 271 " --> pdb=" O LYS U 449 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL U 451 " --> pdb=" O ILE U 271 " (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: 3.707A pdb=" N THR U 593 " --> pdb=" O ILE U 365 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'U' and resid 730 through 733 removed outlier: 6.419A pdb=" N CYS U 499 " --> pdb=" O LEU U 731 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL U 733 " --> pdb=" O CYS U 499 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL U 501 " --> pdb=" O VAL U 733 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'V' and resid 132 through 136 removed outlier: 6.554A pdb=" N VAL V 103 " --> pdb=" O TYR V 133 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER V 135 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU V 105 " --> pdb=" O SER V 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE V 10 " --> pdb=" O THR V 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'V' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'V' and resid 297 through 300 removed outlier: 5.875A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.218A 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 141 removed outlier: 6.660A pdb=" N VAL W 17 " --> pdb=" O LEU W 109 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR W 111 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE W 19 " --> pdb=" O THR W 111 " (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 408 through 411 removed outlier: 5.970A pdb=" N LEU W 156 " --> pdb=" O VAL W 409 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR W 411 " --> pdb=" O LEU W 156 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL W 158 " --> pdb=" O THR W 411 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'W' and resid 269 through 271 Processing sheet with id= M, first strand: chain 'X' and resid 41 through 44 removed outlier: 3.514A pdb=" N GLY X 62 " --> pdb=" O LYS X 44 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'X' and resid 48 through 51 509 hydrogen bonds defined for protein. 1362 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: 3.60 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.34: 3920 1.34 - 1.53: 6323 1.53 - 1.71: 2526 1.71 - 1.89: 76 1.89 - 2.07: 1 Bond restraints: 12846 Sorted by residual: bond pdb=" C4 AGS U 900 " pdb=" C5 AGS U 900 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" O2B AGS W 500 " pdb=" PB AGS W 500 " ideal model delta sigma weight residual 1.531 1.401 0.130 1.60e-02 3.91e+03 6.60e+01 bond pdb=" C5 AGS U 900 " pdb=" C6 AGS U 900 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C ILE U 510 " pdb=" O ILE U 510 " ideal model delta sigma weight residual 1.237 1.312 -0.075 1.07e-02 8.73e+03 4.95e+01 bond pdb=" PG AGS V 500 " pdb=" S1G AGS V 500 " ideal model delta sigma weight residual 1.949 1.815 0.134 2.00e-02 2.50e+03 4.52e+01 ... (remaining 12841 not shown) Histogram of bond angle deviations from ideal: 89.74 - 99.02: 13 99.02 - 108.29: 1068 108.29 - 117.57: 8373 117.57 - 126.84: 7792 126.84 - 136.12: 167 Bond angle restraints: 17413 Sorted by residual: angle pdb=" C5 AGS U 900 " pdb=" C4 AGS U 900 " pdb=" N3 AGS U 900 " ideal model delta sigma weight residual 126.80 118.66 8.14 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C4 AGS U 900 " pdb=" C5 AGS U 900 " pdb=" N7 AGS U 900 " ideal model delta sigma weight residual 110.73 106.58 4.15 4.52e-01 4.89e+00 8.42e+01 angle pdb=" C5 AGS U 900 " pdb=" N7 AGS U 900 " pdb=" C8 AGS U 900 " ideal model delta sigma weight residual 103.67 107.45 -3.78 4.26e-01 5.51e+00 7.86e+01 angle pdb=" N3 AGS U 900 " pdb=" C4 AGS U 900 " pdb=" N9 AGS U 900 " ideal model delta sigma weight residual 127.16 135.02 -7.86 1.06e+00 8.92e-01 5.51e+01 angle pdb=" CA GLY W 412 " pdb=" C GLY W 412 " pdb=" O GLY W 412 " ideal model delta sigma weight residual 121.88 116.71 5.17 7.80e-01 1.64e+00 4.40e+01 ... (remaining 17408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.03: 7484 27.03 - 54.07: 265 54.07 - 81.10: 40 81.10 - 108.13: 3 108.13 - 135.17: 1 Dihedral angle restraints: 7793 sinusoidal: 3239 harmonic: 4554 Sorted by residual: dihedral pdb=" CA GLY W 32 " pdb=" C GLY W 32 " pdb=" N SER W 33 " pdb=" CA SER W 33 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA SER U 522 " pdb=" C SER U 522 " pdb=" N ALA U 523 " pdb=" CA ALA U 523 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL W 158 " pdb=" C VAL W 158 " pdb=" N ASP W 159 " pdb=" CA ASP W 159 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 7790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1171 0.080 - 0.161: 594 0.161 - 0.241: 122 0.241 - 0.322: 35 0.322 - 0.402: 4 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CA ILE U 510 " pdb=" N ILE U 510 " pdb=" C ILE U 510 " pdb=" CB ILE U 510 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA VAL U 451 " pdb=" N VAL U 451 " pdb=" C VAL U 451 " pdb=" CB VAL U 451 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA SER W 143 " pdb=" N SER W 143 " pdb=" C SER W 143 " pdb=" CB SER W 143 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 1923 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 450 " -0.087 2.00e-02 2.50e+03 5.05e-02 5.11e+01 pdb=" CG TYR W 450 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TYR W 450 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR W 450 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR W 450 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR W 450 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR W 450 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR W 450 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS W 162 " -0.062 2.00e-02 2.50e+03 5.23e-02 4.10e+01 pdb=" CG HIS W 162 " 0.105 2.00e-02 2.50e+03 pdb=" ND1 HIS W 162 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS W 162 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS W 162 " -0.034 2.00e-02 2.50e+03 pdb=" NE2 HIS W 162 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP W 469 " 0.079 2.00e-02 2.50e+03 3.84e-02 3.70e+01 pdb=" CG TRP W 469 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP W 469 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP W 469 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP W 469 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP W 469 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP W 469 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 469 " 0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 469 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP W 469 " 0.013 2.00e-02 2.50e+03 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 17 2.57 - 3.15: 9799 3.15 - 3.73: 18094 3.73 - 4.32: 27474 4.32 - 4.90: 45143 Nonbonded interactions: 100527 Sorted by model distance: nonbonded pdb=" O2G AGS W 500 " pdb="MG MG W 501 " model vdw 1.981 2.170 nonbonded pdb=" OD1 ASP U 531 " pdb=" O3' AGS U 900 " model vdw 1.989 2.440 nonbonded pdb=" O2G AGS V 500 " pdb="MG MG V 501 " model vdw 2.087 2.170 nonbonded pdb=" O2B AGS U 900 " pdb="MG MG U 901 " model vdw 2.230 2.170 nonbonded pdb=" O3G AGS U 900 " pdb="MG MG U 901 " model vdw 2.266 2.170 ... (remaining 100522 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: 1.280 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: 4.050 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.030 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.134 12846 Z= 1.052 Angle : 1.875 15.060 17413 Z= 1.320 Chirality : 0.097 0.402 1926 Planarity : 0.010 0.052 2229 Dihedral : 14.338 135.168 4839 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.76 % Favored : 96.04 % Rotamer: Outliers : 0.72 % Allowed : 3.38 % Favored : 95.90 % Cbeta Deviations : 0.14 % 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 (0.20), residues: 1541 helix: -1.33 (0.16), residues: 694 sheet: 0.88 (0.38), residues: 179 loop : -0.35 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.014 TRP W 469 HIS 0.039 0.006 HIS W 162 PHE 0.070 0.013 PHE U 572 TYR 0.098 0.013 TYR W 450 ARG 0.023 0.002 ARG V 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: G 457 MET cc_start: 0.6300 (tpp) cc_final: 0.6021 (tpt) REVERT: G 490 ARG cc_start: 0.5695 (mtt180) cc_final: 0.5300 (ptt-90) REVERT: G 524 GLN cc_start: 0.6742 (mt0) cc_final: 0.6517 (mt0) REVERT: G 545 LYS cc_start: 0.7951 (mttt) cc_final: 0.7553 (tppt) REVERT: U 286 ASP cc_start: 0.7792 (m-30) cc_final: 0.7340 (p0) REVERT: U 287 HIS cc_start: 0.8925 (p90) cc_final: 0.8632 (p-80) REVERT: U 441 LYS cc_start: 0.8094 (mttt) cc_final: 0.7739 (mmtt) REVERT: U 515 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7443 (mm-30) REVERT: U 574 ASP cc_start: 0.8280 (p0) cc_final: 0.8006 (p0) REVERT: U 585 MET cc_start: 0.8662 (mtp) cc_final: 0.8314 (mtm) REVERT: U 591 GLN cc_start: 0.8052 (mt0) cc_final: 0.7787 (mp10) REVERT: U 602 ASP cc_start: 0.7320 (m-30) cc_final: 0.6699 (p0) REVERT: U 618 LYS cc_start: 0.8504 (tttt) cc_final: 0.8253 (tttt) REVERT: U 644 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6982 (mm-30) REVERT: U 655 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7435 (mm-30) REVERT: U 658 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7696 (mm-30) REVERT: U 688 LYS cc_start: 0.7491 (mttt) cc_final: 0.7088 (pttm) REVERT: U 733 VAL cc_start: 0.8054 (t) cc_final: 0.7823 (m) REVERT: U 765 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7590 (mp10) REVERT: U 773 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7460 (mt-10) REVERT: U 809 GLU cc_start: 0.8185 (tt0) cc_final: 0.7916 (tp30) REVERT: U 835 ASP cc_start: 0.8747 (m-30) cc_final: 0.8462 (t70) REVERT: U 853 LYS cc_start: 0.8671 (mttt) cc_final: 0.8346 (mmmt) REVERT: U 856 GLU cc_start: 0.7772 (tt0) cc_final: 0.7377 (tm-30) REVERT: V 25 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7639 (p0) REVERT: V 53 TYR cc_start: 0.8807 (m-80) cc_final: 0.8499 (m-80) REVERT: V 68 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7172 (tpt170) REVERT: V 69 TYR cc_start: 0.8744 (m-80) cc_final: 0.8112 (m-80) REVERT: V 78 ASN cc_start: 0.7921 (t0) cc_final: 0.7713 (t0) REVERT: V 80 ASP cc_start: 0.8545 (m-30) cc_final: 0.8327 (m-30) REVERT: V 99 GLU cc_start: 0.8501 (pt0) cc_final: 0.8250 (pm20) REVERT: V 128 ASN cc_start: 0.8127 (m110) cc_final: 0.7553 (t0) REVERT: V 160 THR cc_start: 0.9228 (m) cc_final: 0.9028 (m) REVERT: V 178 ILE cc_start: 0.8241 (mm) cc_final: 0.7892 (mp) REVERT: V 190 MET cc_start: 0.7813 (mtm) cc_final: 0.7582 (mtm) REVERT: V 222 ASP cc_start: 0.7504 (m-30) cc_final: 0.7221 (t0) REVERT: V 225 GLN cc_start: 0.7525 (mt0) cc_final: 0.6764 (tp-100) REVERT: V 232 GLN cc_start: 0.7569 (mt0) cc_final: 0.7186 (pt0) REVERT: V 246 GLN cc_start: 0.6655 (tt0) cc_final: 0.5828 (mm-40) REVERT: V 270 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8436 (mt-10) REVERT: V 291 LYS cc_start: 0.8185 (mttt) cc_final: 0.7983 (mtpp) REVERT: V 292 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7843 (mp0) REVERT: V 305 MET cc_start: 0.8921 (mmm) cc_final: 0.8581 (mmm) REVERT: V 326 LYS cc_start: 0.8338 (tttt) cc_final: 0.7916 (tptp) REVERT: V 360 GLN cc_start: 0.8331 (tt0) cc_final: 0.7856 (mp10) REVERT: W 91 GLN cc_start: 0.8064 (tt0) cc_final: 0.7654 (tp40) REVERT: W 101 ASN cc_start: 0.8570 (t0) cc_final: 0.8121 (p0) REVERT: W 132 MET cc_start: 0.8062 (mtm) cc_final: 0.7708 (mtp) REVERT: W 152 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8220 (mmm160) REVERT: W 172 ASP cc_start: 0.8366 (m-30) cc_final: 0.8155 (m-30) REVERT: W 196 LYS cc_start: 0.7869 (tttt) cc_final: 0.7283 (pttm) REVERT: W 215 GLU cc_start: 0.6634 (mt-10) cc_final: 0.5988 (mp0) REVERT: W 224 GLU cc_start: 0.8210 (tt0) cc_final: 0.7937 (tp30) REVERT: W 256 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7699 (tm-30) REVERT: W 277 GLU cc_start: 0.8873 (tt0) cc_final: 0.8317 (mp0) REVERT: W 394 MET cc_start: 0.7822 (mmt) cc_final: 0.7602 (mmm) REVERT: W 399 ASP cc_start: 0.8403 (m-30) cc_final: 0.8073 (p0) REVERT: W 473 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7272 (ttmt) REVERT: X 51 LYS cc_start: 0.8457 (tttt) cc_final: 0.8181 (ttmm) outliers start: 10 outliers final: 5 residues processed: 297 average time/residue: 0.2865 time to fit residues: 116.3145 Evaluate side-chains 214 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 208 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain V residue 25 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 464 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 468 HIS G 518 GLN U 272 HIS U 324 ASN U 369 ASN U 502 ASN U 799 GLN V 115 ASN V 232 GLN W 95 GLN X 45 ASN X 59 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12846 Z= 0.193 Angle : 0.591 8.133 17413 Z= 0.315 Chirality : 0.044 0.143 1926 Planarity : 0.004 0.039 2229 Dihedral : 9.224 138.464 1742 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 1.73 % Allowed : 6.84 % Favored : 91.43 % 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: 0.62 (0.21), residues: 1541 helix: 0.58 (0.19), residues: 696 sheet: 1.05 (0.36), residues: 210 loop : 0.19 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.023 0.002 PHE U 598 TYR 0.014 0.001 TYR W 69 ARG 0.003 0.000 ARG V 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 1.452 Fit side-chains REVERT: G 457 MET cc_start: 0.6474 (tpp) cc_final: 0.6172 (tpt) REVERT: G 490 ARG cc_start: 0.5865 (mtt180) cc_final: 0.5249 (ptt-90) REVERT: G 545 LYS cc_start: 0.7860 (mttt) cc_final: 0.7460 (tppt) REVERT: U 286 ASP cc_start: 0.7869 (m-30) cc_final: 0.7532 (t70) REVERT: U 441 LYS cc_start: 0.7923 (mttt) cc_final: 0.7606 (mmtm) REVERT: U 515 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7390 (mm-30) REVERT: U 574 ASP cc_start: 0.8189 (p0) cc_final: 0.7952 (p0) REVERT: U 591 GLN cc_start: 0.7500 (mt0) cc_final: 0.7294 (mp10) REVERT: U 618 LYS cc_start: 0.8300 (tttt) cc_final: 0.8058 (tttt) REVERT: U 644 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6726 (mm-30) REVERT: U 658 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7322 (mm-30) REVERT: U 670 LYS cc_start: 0.6871 (tttt) cc_final: 0.6489 (mmmt) REVERT: U 688 LYS cc_start: 0.7436 (mttt) cc_final: 0.6945 (pttm) REVERT: U 765 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7550 (mp10) REVERT: U 773 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7340 (mt-10) REVERT: U 835 ASP cc_start: 0.8562 (m-30) cc_final: 0.8274 (t0) REVERT: V 25 ASP cc_start: 0.8210 (t0) cc_final: 0.7543 (p0) REVERT: V 68 ARG cc_start: 0.7602 (mtp180) cc_final: 0.6840 (ttt90) REVERT: V 69 TYR cc_start: 0.8744 (m-80) cc_final: 0.8273 (m-80) REVERT: V 99 GLU cc_start: 0.8331 (pt0) cc_final: 0.8052 (pm20) REVERT: V 128 ASN cc_start: 0.7989 (m110) cc_final: 0.7512 (t0) REVERT: V 222 ASP cc_start: 0.7469 (m-30) cc_final: 0.7203 (t0) REVERT: V 225 GLN cc_start: 0.7494 (mt0) cc_final: 0.6774 (tp-100) REVERT: V 246 GLN cc_start: 0.6292 (tt0) cc_final: 0.5645 (mm-40) REVERT: V 270 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8240 (mt-10) REVERT: V 292 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8000 (mp0) REVERT: V 305 MET cc_start: 0.8503 (mmm) cc_final: 0.8010 (mmm) REVERT: V 326 LYS cc_start: 0.8365 (tttt) cc_final: 0.7924 (tmtt) REVERT: W 34 ASP cc_start: 0.8344 (m-30) cc_final: 0.7859 (p0) REVERT: W 91 GLN cc_start: 0.7832 (tt0) cc_final: 0.7470 (tp-100) REVERT: W 101 ASN cc_start: 0.8480 (t0) cc_final: 0.8095 (p0) REVERT: W 196 LYS cc_start: 0.7709 (tttt) cc_final: 0.7052 (pttm) REVERT: W 210 LYS cc_start: 0.8116 (mttt) cc_final: 0.7590 (tmtt) REVERT: W 224 GLU cc_start: 0.8115 (tt0) cc_final: 0.7866 (tp30) REVERT: W 256 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7554 (tm-30) REVERT: W 277 GLU cc_start: 0.8680 (tt0) cc_final: 0.8235 (mp0) REVERT: W 394 MET cc_start: 0.7773 (mmt) cc_final: 0.7543 (mmm) REVERT: W 399 ASP cc_start: 0.8527 (m-30) cc_final: 0.8236 (p0) REVERT: W 481 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7909 (mp0) REVERT: X 51 LYS cc_start: 0.8430 (tttt) cc_final: 0.8196 (ttmm) outliers start: 24 outliers final: 14 residues processed: 243 average time/residue: 0.2542 time to fit residues: 88.0374 Evaluate side-chains 204 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 666 ASN Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain U residue 800 ILE Chi-restraints excluded: chain V residue 267 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 0.0270 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 287 HIS V 78 ASN V 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12846 Z= 0.223 Angle : 0.544 8.254 17413 Z= 0.284 Chirality : 0.044 0.162 1926 Planarity : 0.004 0.045 2229 Dihedral : 8.875 146.996 1737 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 1.80 % Allowed : 9.36 % Favored : 88.84 % 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: 0.86 (0.21), residues: 1541 helix: 0.90 (0.20), residues: 702 sheet: 0.78 (0.35), residues: 214 loop : 0.31 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 356 HIS 0.004 0.001 HIS U 823 PHE 0.020 0.002 PHE U 546 TYR 0.017 0.001 TYR W 450 ARG 0.003 0.000 ARG W 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.477 Fit side-chains REVERT: G 490 ARG cc_start: 0.5879 (mtt180) cc_final: 0.5250 (ptt180) REVERT: G 545 LYS cc_start: 0.7865 (mttt) cc_final: 0.7545 (tptt) REVERT: U 286 ASP cc_start: 0.7815 (m-30) cc_final: 0.7474 (t70) REVERT: U 375 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7559 (mp0) REVERT: U 441 LYS cc_start: 0.7915 (mttt) cc_final: 0.7692 (mmtm) REVERT: U 515 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7419 (mm-30) REVERT: U 574 ASP cc_start: 0.8170 (p0) cc_final: 0.7894 (p0) REVERT: U 644 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6620 (tp30) REVERT: U 658 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7246 (mm-30) REVERT: U 688 LYS cc_start: 0.7369 (mttt) cc_final: 0.6936 (pttm) REVERT: U 765 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7648 (mp10) REVERT: U 773 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7335 (mt-10) REVERT: U 835 ASP cc_start: 0.8631 (m-30) cc_final: 0.8304 (t0) REVERT: V 25 ASP cc_start: 0.8177 (t0) cc_final: 0.7535 (p0) REVERT: V 68 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7388 (mtp-110) REVERT: V 69 TYR cc_start: 0.8764 (m-80) cc_final: 0.8377 (m-80) REVERT: V 99 GLU cc_start: 0.8395 (pt0) cc_final: 0.8085 (pm20) REVERT: V 128 ASN cc_start: 0.8233 (m110) cc_final: 0.7658 (t0) REVERT: V 160 THR cc_start: 0.9149 (m) cc_final: 0.8835 (m) REVERT: V 222 ASP cc_start: 0.7451 (m-30) cc_final: 0.7044 (t70) REVERT: V 225 GLN cc_start: 0.7519 (mt0) cc_final: 0.6901 (tp-100) REVERT: V 246 GLN cc_start: 0.6269 (tt0) cc_final: 0.5578 (mm-40) REVERT: V 270 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8202 (mt-10) REVERT: V 292 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8084 (mp0) REVERT: V 326 LYS cc_start: 0.8367 (tttt) cc_final: 0.7918 (tmtt) REVERT: W 91 GLN cc_start: 0.7748 (tt0) cc_final: 0.7433 (tp-100) REVERT: W 101 ASN cc_start: 0.8483 (t0) cc_final: 0.8181 (p0) REVERT: W 196 LYS cc_start: 0.7754 (tttt) cc_final: 0.7077 (pttm) REVERT: W 210 LYS cc_start: 0.8119 (mttt) cc_final: 0.7546 (tmtt) REVERT: W 215 GLU cc_start: 0.6305 (mt-10) cc_final: 0.5849 (mp0) REVERT: W 224 GLU cc_start: 0.8096 (tt0) cc_final: 0.7835 (tp30) REVERT: W 256 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7404 (tm-30) REVERT: W 277 GLU cc_start: 0.8664 (tt0) cc_final: 0.8273 (mp0) REVERT: W 399 ASP cc_start: 0.8507 (m-30) cc_final: 0.8256 (p0) REVERT: W 425 MET cc_start: 0.7268 (tpt) cc_final: 0.6767 (tpt) REVERT: W 428 LEU cc_start: 0.8043 (mm) cc_final: 0.7813 (mm) REVERT: W 430 LYS cc_start: 0.6612 (mttt) cc_final: 0.6331 (mptt) REVERT: W 481 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7916 (mp0) REVERT: X 51 LYS cc_start: 0.8308 (tttt) cc_final: 0.8066 (ttmm) outliers start: 25 outliers final: 18 residues processed: 213 average time/residue: 0.2649 time to fit residues: 80.3497 Evaluate side-chains 195 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 287 HIS Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 581 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 800 ILE Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 462 LEU Chi-restraints excluded: chain W residue 464 THR 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: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN U 792 ASN V 78 ASN W 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12846 Z= 0.293 Angle : 0.547 6.296 17413 Z= 0.284 Chirality : 0.045 0.145 1926 Planarity : 0.005 0.044 2229 Dihedral : 9.087 157.885 1736 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 1.80 % Allowed : 11.09 % Favored : 87.11 % 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: 0.75 (0.21), residues: 1541 helix: 0.86 (0.19), residues: 699 sheet: 0.71 (0.36), residues: 211 loop : 0.18 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 356 HIS 0.005 0.001 HIS V 161 PHE 0.017 0.002 PHE U 546 TYR 0.020 0.002 TYR W 450 ARG 0.003 0.000 ARG W 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.585 Fit side-chains REVERT: G 457 MET cc_start: 0.6428 (tpt) cc_final: 0.6189 (tpt) REVERT: G 490 ARG cc_start: 0.5929 (mtt180) cc_final: 0.5304 (ptt-90) REVERT: G 524 GLN cc_start: 0.6526 (mt0) cc_final: 0.6305 (mt0) REVERT: G 545 LYS cc_start: 0.7857 (mttt) cc_final: 0.7526 (tppt) REVERT: U 286 ASP cc_start: 0.8165 (m-30) cc_final: 0.7963 (t70) REVERT: U 375 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7505 (mp0) REVERT: U 441 LYS cc_start: 0.7912 (mttt) cc_final: 0.7688 (mmtm) REVERT: U 515 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7449 (mm-30) REVERT: U 574 ASP cc_start: 0.8190 (p0) cc_final: 0.7902 (p0) REVERT: U 605 MET cc_start: 0.8521 (ttt) cc_final: 0.8318 (ttt) REVERT: U 644 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6570 (tp30) REVERT: U 688 LYS cc_start: 0.7395 (mttt) cc_final: 0.6988 (pttm) REVERT: U 765 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7635 (mp10) REVERT: U 773 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7332 (mt-10) REVERT: U 835 ASP cc_start: 0.8647 (m-30) cc_final: 0.8308 (t0) REVERT: V 25 ASP cc_start: 0.8177 (t0) cc_final: 0.7545 (p0) REVERT: V 68 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7357 (mtp-110) REVERT: V 69 TYR cc_start: 0.8819 (m-80) cc_final: 0.8405 (m-80) REVERT: V 128 ASN cc_start: 0.8280 (m110) cc_final: 0.7677 (t0) REVERT: V 160 THR cc_start: 0.9175 (m) cc_final: 0.8887 (m) REVERT: V 222 ASP cc_start: 0.7339 (m-30) cc_final: 0.7092 (t0) REVERT: V 225 GLN cc_start: 0.7541 (mt0) cc_final: 0.6856 (tp-100) REVERT: V 246 GLN cc_start: 0.6283 (tt0) cc_final: 0.5592 (mm-40) REVERT: V 270 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8195 (mt-10) REVERT: V 292 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8057 (mp0) REVERT: V 326 LYS cc_start: 0.8150 (tttt) cc_final: 0.7678 (tmtt) REVERT: W 91 GLN cc_start: 0.7776 (tt0) cc_final: 0.7427 (tp-100) REVERT: W 101 ASN cc_start: 0.8480 (t0) cc_final: 0.8186 (p0) REVERT: W 196 LYS cc_start: 0.7700 (tttt) cc_final: 0.7311 (ttpt) REVERT: W 210 LYS cc_start: 0.8165 (mttt) cc_final: 0.7619 (tmtt) REVERT: W 215 GLU cc_start: 0.6407 (mt-10) cc_final: 0.5939 (mp0) REVERT: W 224 GLU cc_start: 0.8103 (tt0) cc_final: 0.7840 (tp30) REVERT: W 256 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7394 (tm-30) REVERT: W 277 GLU cc_start: 0.8652 (tt0) cc_final: 0.8218 (mp0) REVERT: W 399 ASP cc_start: 0.8467 (m-30) cc_final: 0.8228 (p0) REVERT: W 425 MET cc_start: 0.7194 (tpt) cc_final: 0.6675 (tpt) REVERT: W 428 LEU cc_start: 0.8034 (mm) cc_final: 0.7819 (mm) REVERT: W 430 LYS cc_start: 0.6745 (mttt) cc_final: 0.6420 (mmtt) REVERT: W 481 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7914 (mp0) REVERT: X 51 LYS cc_start: 0.8291 (tttt) cc_final: 0.8053 (ttmm) outliers start: 25 outliers final: 20 residues processed: 196 average time/residue: 0.2645 time to fit residues: 74.8523 Evaluate side-chains 189 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 287 HIS Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain U residue 800 ILE Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 202 THR Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 462 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 287 HIS V 78 ASN W 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12846 Z= 0.189 Angle : 0.485 5.972 17413 Z= 0.253 Chirality : 0.043 0.137 1926 Planarity : 0.004 0.045 2229 Dihedral : 8.896 166.375 1736 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.94 % Allowed : 11.38 % Favored : 86.68 % 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: 0.86 (0.21), residues: 1541 helix: 1.05 (0.20), residues: 699 sheet: 0.62 (0.36), residues: 199 loop : 0.18 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 356 HIS 0.004 0.001 HIS U 287 PHE 0.013 0.001 PHE W 207 TYR 0.013 0.001 TYR W 450 ARG 0.002 0.000 ARG V 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.596 Fit side-chains REVERT: G 457 MET cc_start: 0.6258 (tpt) cc_final: 0.5982 (tpt) REVERT: G 490 ARG cc_start: 0.5891 (mtt180) cc_final: 0.5245 (ptt180) REVERT: G 524 GLN cc_start: 0.6659 (mt0) cc_final: 0.6428 (mt0) REVERT: G 545 LYS cc_start: 0.7857 (mttt) cc_final: 0.7532 (tppt) REVERT: U 286 ASP cc_start: 0.8150 (m-30) cc_final: 0.7817 (t70) REVERT: U 375 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7825 (mt-10) REVERT: U 441 LYS cc_start: 0.7870 (mttt) cc_final: 0.7644 (mmtm) REVERT: U 515 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7419 (mm-30) REVERT: U 574 ASP cc_start: 0.8138 (p0) cc_final: 0.7896 (p0) REVERT: U 688 LYS cc_start: 0.7389 (mttt) cc_final: 0.6992 (pttm) REVERT: U 765 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7632 (mp10) REVERT: U 773 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7267 (mt-10) REVERT: U 835 ASP cc_start: 0.8618 (m-30) cc_final: 0.8261 (t0) REVERT: V 25 ASP cc_start: 0.8123 (t0) cc_final: 0.7477 (p0) REVERT: V 68 ARG cc_start: 0.7607 (mtp180) cc_final: 0.7351 (mtp-110) REVERT: V 69 TYR cc_start: 0.8807 (m-80) cc_final: 0.8381 (m-80) REVERT: V 128 ASN cc_start: 0.8258 (m110) cc_final: 0.7667 (t0) REVERT: V 160 THR cc_start: 0.9170 (m) cc_final: 0.8907 (m) REVERT: V 222 ASP cc_start: 0.7377 (m-30) cc_final: 0.7155 (t0) REVERT: V 225 GLN cc_start: 0.7462 (mt0) cc_final: 0.6809 (tp40) REVERT: V 246 GLN cc_start: 0.6373 (tt0) cc_final: 0.5704 (mm-40) REVERT: V 270 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8164 (mt-10) REVERT: V 292 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8085 (mp0) REVERT: V 326 LYS cc_start: 0.8148 (tttt) cc_final: 0.7681 (tmtt) REVERT: W 34 ASP cc_start: 0.8350 (m-30) cc_final: 0.7827 (p0) REVERT: W 91 GLN cc_start: 0.7755 (tt0) cc_final: 0.7428 (tp-100) REVERT: W 101 ASN cc_start: 0.8437 (t0) cc_final: 0.8175 (p0) REVERT: W 182 ARG cc_start: 0.8237 (ptt180) cc_final: 0.8005 (ttp80) REVERT: W 196 LYS cc_start: 0.7691 (tttt) cc_final: 0.7315 (ttpt) REVERT: W 210 LYS cc_start: 0.8200 (mttt) cc_final: 0.7647 (tmtt) REVERT: W 224 GLU cc_start: 0.8143 (tt0) cc_final: 0.7844 (tp30) REVERT: W 256 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7370 (tm-30) REVERT: W 277 GLU cc_start: 0.8642 (tt0) cc_final: 0.8202 (mp0) REVERT: W 291 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6605 (tt0) REVERT: W 399 ASP cc_start: 0.8634 (m-30) cc_final: 0.8337 (p0) REVERT: W 425 MET cc_start: 0.7184 (tpt) cc_final: 0.6668 (tpt) REVERT: W 430 LYS cc_start: 0.6638 (mttt) cc_final: 0.6367 (mmtt) REVERT: W 481 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7923 (mp0) REVERT: X 51 LYS cc_start: 0.8247 (tttt) cc_final: 0.8000 (ttmm) outliers start: 27 outliers final: 20 residues processed: 206 average time/residue: 0.2632 time to fit residues: 77.5274 Evaluate side-chains 190 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 287 HIS Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain U residue 807 GLU Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 291 GLU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN U 287 HIS V 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12846 Z= 0.216 Angle : 0.485 5.470 17413 Z= 0.252 Chirality : 0.043 0.136 1926 Planarity : 0.004 0.043 2229 Dihedral : 8.827 167.869 1736 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 2.45 % Allowed : 11.88 % Favored : 85.67 % 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: 0.86 (0.21), residues: 1541 helix: 1.06 (0.20), residues: 699 sheet: 0.64 (0.37), residues: 199 loop : 0.16 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 356 HIS 0.004 0.001 HIS V 161 PHE 0.012 0.001 PHE W 207 TYR 0.016 0.001 TYR W 450 ARG 0.002 0.000 ARG W 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: G 457 MET cc_start: 0.6149 (tpt) cc_final: 0.5872 (tpt) REVERT: G 490 ARG cc_start: 0.5913 (mtt180) cc_final: 0.5252 (ptt180) REVERT: G 524 GLN cc_start: 0.6638 (mt0) cc_final: 0.6388 (mt0) REVERT: G 545 LYS cc_start: 0.7848 (mttt) cc_final: 0.7527 (tppt) REVERT: U 286 ASP cc_start: 0.8073 (m-30) cc_final: 0.7763 (t70) REVERT: U 375 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7827 (mt-10) REVERT: U 441 LYS cc_start: 0.7874 (mttt) cc_final: 0.7648 (mmtm) REVERT: U 515 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7357 (mm-30) REVERT: U 574 ASP cc_start: 0.8175 (p0) cc_final: 0.7891 (p0) REVERT: U 688 LYS cc_start: 0.7366 (mttt) cc_final: 0.6895 (pttm) REVERT: U 765 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7657 (mp10) REVERT: U 835 ASP cc_start: 0.8618 (m-30) cc_final: 0.8253 (t0) REVERT: V 25 ASP cc_start: 0.8117 (t0) cc_final: 0.7479 (p0) REVERT: V 68 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7352 (mtp-110) REVERT: V 69 TYR cc_start: 0.8814 (m-80) cc_final: 0.8389 (m-80) REVERT: V 160 THR cc_start: 0.9186 (m) cc_final: 0.8930 (m) REVERT: V 222 ASP cc_start: 0.7347 (m-30) cc_final: 0.7134 (t0) REVERT: V 225 GLN cc_start: 0.7460 (mt0) cc_final: 0.6807 (tp40) REVERT: V 246 GLN cc_start: 0.6454 (tt0) cc_final: 0.5772 (mm-40) REVERT: V 270 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8152 (mt-10) REVERT: V 292 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8030 (mp0) REVERT: V 326 LYS cc_start: 0.8131 (tttt) cc_final: 0.7662 (tmtt) REVERT: W 34 ASP cc_start: 0.8368 (m-30) cc_final: 0.7835 (p0) REVERT: W 91 GLN cc_start: 0.7773 (tt0) cc_final: 0.7435 (tp-100) REVERT: W 101 ASN cc_start: 0.8435 (t0) cc_final: 0.8183 (p0) REVERT: W 182 ARG cc_start: 0.8277 (ptt180) cc_final: 0.7986 (ttp80) REVERT: W 196 LYS cc_start: 0.7689 (tttt) cc_final: 0.7304 (ttpt) REVERT: W 210 LYS cc_start: 0.8186 (mttt) cc_final: 0.7632 (tmtt) REVERT: W 215 GLU cc_start: 0.6218 (mt-10) cc_final: 0.5799 (mp0) REVERT: W 224 GLU cc_start: 0.8128 (tt0) cc_final: 0.7842 (tp30) REVERT: W 256 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7345 (tm-30) REVERT: W 277 GLU cc_start: 0.8640 (tt0) cc_final: 0.8206 (mp0) REVERT: W 291 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: W 292 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7574 (tt) REVERT: W 399 ASP cc_start: 0.8634 (m-30) cc_final: 0.8351 (p0) REVERT: W 425 MET cc_start: 0.7188 (tpt) cc_final: 0.6682 (tpt) REVERT: W 430 LYS cc_start: 0.6697 (mttt) cc_final: 0.6429 (mmtt) REVERT: W 481 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7909 (mp0) REVERT: X 51 LYS cc_start: 0.8243 (tttt) cc_final: 0.7994 (ttmm) outliers start: 34 outliers final: 28 residues processed: 197 average time/residue: 0.2637 time to fit residues: 74.3891 Evaluate side-chains 197 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 287 HIS Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 666 ASN Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain U residue 801 LYS Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 291 GLU Chi-restraints excluded: chain W residue 292 LEU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 108 optimal weight: 0.0970 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 287 HIS U 818 GLN U 821 ASN V 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12846 Z= 0.137 Angle : 0.451 5.426 17413 Z= 0.235 Chirality : 0.042 0.139 1926 Planarity : 0.004 0.041 2229 Dihedral : 8.579 168.883 1736 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 2.02 % Allowed : 12.53 % Favored : 85.46 % 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: 1.10 (0.22), residues: 1541 helix: 1.28 (0.20), residues: 695 sheet: 0.82 (0.37), residues: 203 loop : 0.22 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 356 HIS 0.006 0.001 HIS U 287 PHE 0.013 0.001 PHE W 207 TYR 0.011 0.001 TYR U 596 ARG 0.002 0.000 ARG W 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.482 Fit side-chains REVERT: G 457 MET cc_start: 0.6109 (tpt) cc_final: 0.5832 (tpt) REVERT: G 490 ARG cc_start: 0.5823 (mtt180) cc_final: 0.5077 (ptt180) REVERT: G 524 GLN cc_start: 0.6717 (mt0) cc_final: 0.6401 (mt0) REVERT: G 545 LYS cc_start: 0.7846 (mttt) cc_final: 0.7532 (tptt) REVERT: U 286 ASP cc_start: 0.8102 (m-30) cc_final: 0.7649 (t70) REVERT: U 375 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7787 (mt-10) REVERT: U 441 LYS cc_start: 0.7848 (mttt) cc_final: 0.7620 (mmtm) REVERT: U 515 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7346 (mm-30) REVERT: U 574 ASP cc_start: 0.8169 (p0) cc_final: 0.7885 (p0) REVERT: U 631 GLU cc_start: 0.8013 (tt0) cc_final: 0.7810 (mt-10) REVERT: U 688 LYS cc_start: 0.7319 (mttt) cc_final: 0.6859 (pttm) REVERT: U 765 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7654 (mp10) REVERT: U 801 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7831 (mttp) REVERT: U 835 ASP cc_start: 0.8607 (m-30) cc_final: 0.8250 (t0) REVERT: U 853 LYS cc_start: 0.8080 (mttt) cc_final: 0.7749 (mmmt) REVERT: V 25 ASP cc_start: 0.8095 (t0) cc_final: 0.7455 (p0) REVERT: V 68 ARG cc_start: 0.7593 (mtp180) cc_final: 0.7324 (mtp-110) REVERT: V 69 TYR cc_start: 0.8815 (m-80) cc_final: 0.8381 (m-80) REVERT: V 128 ASN cc_start: 0.8185 (m110) cc_final: 0.7564 (t0) REVERT: V 160 THR cc_start: 0.9171 (m) cc_final: 0.8922 (m) REVERT: V 222 ASP cc_start: 0.7372 (m-30) cc_final: 0.7169 (t0) REVERT: V 225 GLN cc_start: 0.7445 (mt0) cc_final: 0.6804 (tp40) REVERT: V 246 GLN cc_start: 0.6485 (tt0) cc_final: 0.5791 (mm-40) REVERT: V 270 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8141 (mt-10) REVERT: V 292 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8009 (mp0) REVERT: V 326 LYS cc_start: 0.8106 (tttt) cc_final: 0.7657 (tmtt) REVERT: W 34 ASP cc_start: 0.8408 (m-30) cc_final: 0.7862 (p0) REVERT: W 91 GLN cc_start: 0.7744 (tt0) cc_final: 0.7430 (tp-100) REVERT: W 101 ASN cc_start: 0.8423 (t0) cc_final: 0.8182 (p0) REVERT: W 182 ARG cc_start: 0.8230 (ptt180) cc_final: 0.7995 (ttp80) REVERT: W 196 LYS cc_start: 0.7686 (tttt) cc_final: 0.7299 (ttpt) REVERT: W 210 LYS cc_start: 0.8175 (mttt) cc_final: 0.7603 (tmtt) REVERT: W 224 GLU cc_start: 0.8121 (tt0) cc_final: 0.7828 (tp30) REVERT: W 256 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7236 (tm-30) REVERT: W 277 GLU cc_start: 0.8636 (tt0) cc_final: 0.8197 (mp0) REVERT: W 399 ASP cc_start: 0.8637 (m-30) cc_final: 0.8336 (p0) REVERT: W 425 MET cc_start: 0.7184 (tpt) cc_final: 0.6684 (tpt) REVERT: W 430 LYS cc_start: 0.6695 (mttt) cc_final: 0.6427 (mmtt) REVERT: W 481 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7903 (mp0) REVERT: X 51 LYS cc_start: 0.8192 (tttt) cc_final: 0.7943 (ttmm) outliers start: 28 outliers final: 23 residues processed: 192 average time/residue: 0.2668 time to fit residues: 72.8332 Evaluate side-chains 195 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 609 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 666 ASN Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain U residue 801 LYS Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12846 Z= 0.173 Angle : 0.457 5.463 17413 Z= 0.238 Chirality : 0.042 0.139 1926 Planarity : 0.004 0.040 2229 Dihedral : 8.492 168.704 1736 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 2.30 % Allowed : 12.53 % Favored : 85.17 % 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: 1.11 (0.22), residues: 1541 helix: 1.35 (0.20), residues: 689 sheet: 0.77 (0.37), residues: 197 loop : 0.20 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 356 HIS 0.004 0.001 HIS U 823 PHE 0.012 0.001 PHE U 584 TYR 0.013 0.001 TYR W 450 ARG 0.002 0.000 ARG W 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.546 Fit side-chains REVERT: G 457 MET cc_start: 0.6121 (tpt) cc_final: 0.5869 (tpt) REVERT: G 490 ARG cc_start: 0.5979 (mtt180) cc_final: 0.5302 (ptt180) REVERT: G 524 GLN cc_start: 0.6650 (mt0) cc_final: 0.6387 (mt0) REVERT: G 545 LYS cc_start: 0.7859 (mttt) cc_final: 0.7549 (tptt) REVERT: U 286 ASP cc_start: 0.7991 (m-30) cc_final: 0.7628 (t70) REVERT: U 375 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7788 (mt-10) REVERT: U 441 LYS cc_start: 0.7859 (mttt) cc_final: 0.7633 (mmtm) REVERT: U 515 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7354 (mm-30) REVERT: U 574 ASP cc_start: 0.8175 (p0) cc_final: 0.7896 (p0) REVERT: U 688 LYS cc_start: 0.7376 (mttt) cc_final: 0.6914 (pttm) REVERT: U 765 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7607 (mp10) REVERT: U 801 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7834 (mttp) REVERT: U 809 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7547 (tp30) REVERT: U 835 ASP cc_start: 0.8608 (m-30) cc_final: 0.8248 (t0) REVERT: U 853 LYS cc_start: 0.8077 (mttt) cc_final: 0.7743 (mmmt) REVERT: V 25 ASP cc_start: 0.8093 (t0) cc_final: 0.7464 (p0) REVERT: V 68 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7439 (mtp-110) REVERT: V 69 TYR cc_start: 0.8895 (m-80) cc_final: 0.8529 (m-80) REVERT: V 160 THR cc_start: 0.9178 (m) cc_final: 0.8886 (m) REVERT: V 225 GLN cc_start: 0.7503 (mt0) cc_final: 0.6861 (tp40) REVERT: V 246 GLN cc_start: 0.6577 (tt0) cc_final: 0.5895 (mm-40) REVERT: V 270 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8145 (mt-10) REVERT: V 292 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8052 (mp0) REVERT: V 326 LYS cc_start: 0.8107 (tttt) cc_final: 0.7662 (tmtt) REVERT: W 34 ASP cc_start: 0.8418 (m-30) cc_final: 0.7911 (p0) REVERT: W 91 GLN cc_start: 0.7797 (tt0) cc_final: 0.7423 (tp-100) REVERT: W 101 ASN cc_start: 0.8431 (t0) cc_final: 0.8200 (p0) REVERT: W 182 ARG cc_start: 0.8249 (ptt180) cc_final: 0.8008 (ptt90) REVERT: W 196 LYS cc_start: 0.7651 (tttt) cc_final: 0.7277 (ttpt) REVERT: W 210 LYS cc_start: 0.8250 (mttt) cc_final: 0.7634 (tmtt) REVERT: W 224 GLU cc_start: 0.8170 (tt0) cc_final: 0.7865 (tp30) REVERT: W 256 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7253 (tm-30) REVERT: W 277 GLU cc_start: 0.8663 (tt0) cc_final: 0.8223 (mp0) REVERT: W 291 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6443 (tp30) REVERT: W 399 ASP cc_start: 0.8685 (m-30) cc_final: 0.8406 (p0) REVERT: W 425 MET cc_start: 0.7174 (tpt) cc_final: 0.6675 (tpt) REVERT: W 430 LYS cc_start: 0.6757 (mttt) cc_final: 0.6459 (mmtt) REVERT: W 481 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7903 (mp0) REVERT: X 51 LYS cc_start: 0.8182 (tttt) cc_final: 0.7927 (ttmm) outliers start: 32 outliers final: 26 residues processed: 196 average time/residue: 0.2635 time to fit residues: 73.7686 Evaluate side-chains 198 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 666 ASN Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain U residue 801 LYS Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 291 GLU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12846 Z= 0.160 Angle : 0.452 5.431 17413 Z= 0.235 Chirality : 0.042 0.139 1926 Planarity : 0.004 0.039 2229 Dihedral : 8.392 169.029 1736 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 2.23 % Allowed : 12.96 % Favored : 84.81 % 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: 1.16 (0.22), residues: 1541 helix: 1.39 (0.20), residues: 689 sheet: 0.80 (0.37), residues: 202 loop : 0.21 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 356 HIS 0.004 0.001 HIS U 823 PHE 0.012 0.001 PHE U 584 TYR 0.012 0.001 TYR W 450 ARG 0.003 0.000 ARG U 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.581 Fit side-chains REVERT: G 457 MET cc_start: 0.5942 (tpt) cc_final: 0.5682 (tpt) REVERT: G 480 MET cc_start: 0.6969 (mtt) cc_final: 0.6461 (mtt) REVERT: G 524 GLN cc_start: 0.6633 (mt0) cc_final: 0.6351 (mt0) REVERT: G 545 LYS cc_start: 0.7871 (mttt) cc_final: 0.7568 (tptt) REVERT: U 286 ASP cc_start: 0.7971 (m-30) cc_final: 0.7603 (t70) REVERT: U 375 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7778 (mt-10) REVERT: U 441 LYS cc_start: 0.7838 (mttt) cc_final: 0.7605 (mmtm) REVERT: U 515 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7346 (mm-30) REVERT: U 574 ASP cc_start: 0.8166 (p0) cc_final: 0.7895 (p0) REVERT: U 688 LYS cc_start: 0.7384 (mttt) cc_final: 0.6919 (pttm) REVERT: U 765 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7606 (mp10) REVERT: U 801 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7832 (mttp) REVERT: U 835 ASP cc_start: 0.8583 (m-30) cc_final: 0.8238 (t0) REVERT: U 853 LYS cc_start: 0.8067 (mttt) cc_final: 0.7734 (mmmt) REVERT: V 25 ASP cc_start: 0.8088 (t0) cc_final: 0.7466 (p0) REVERT: V 68 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7441 (mtp-110) REVERT: V 69 TYR cc_start: 0.8883 (m-80) cc_final: 0.8519 (m-80) REVERT: V 160 THR cc_start: 0.9189 (m) cc_final: 0.8898 (m) REVERT: V 225 GLN cc_start: 0.7516 (mt0) cc_final: 0.6851 (tp-100) REVERT: V 246 GLN cc_start: 0.6694 (tt0) cc_final: 0.6033 (mm-40) REVERT: V 270 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8123 (mt-10) REVERT: V 292 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8057 (mp0) REVERT: V 326 LYS cc_start: 0.8104 (tttt) cc_final: 0.7657 (tmtt) REVERT: W 34 ASP cc_start: 0.8432 (m-30) cc_final: 0.7896 (p0) REVERT: W 91 GLN cc_start: 0.7783 (tt0) cc_final: 0.7447 (tp-100) REVERT: W 101 ASN cc_start: 0.8441 (t0) cc_final: 0.8221 (p0) REVERT: W 182 ARG cc_start: 0.8249 (ptt180) cc_final: 0.8002 (ptt90) REVERT: W 196 LYS cc_start: 0.7666 (tttt) cc_final: 0.7287 (ttpt) REVERT: W 210 LYS cc_start: 0.8250 (mttt) cc_final: 0.7634 (tmtt) REVERT: W 224 GLU cc_start: 0.8168 (tt0) cc_final: 0.7867 (tp30) REVERT: W 256 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7233 (tm-30) REVERT: W 277 GLU cc_start: 0.8673 (tt0) cc_final: 0.8241 (mp0) REVERT: W 291 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6479 (tp30) REVERT: W 399 ASP cc_start: 0.8724 (m-30) cc_final: 0.8439 (p0) REVERT: W 425 MET cc_start: 0.7197 (tpt) cc_final: 0.6719 (tpt) REVERT: W 430 LYS cc_start: 0.6810 (mttt) cc_final: 0.6503 (mmtt) REVERT: W 481 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7882 (mp0) REVERT: X 51 LYS cc_start: 0.8145 (tttt) cc_final: 0.7886 (ttmm) outliers start: 31 outliers final: 26 residues processed: 196 average time/residue: 0.2605 time to fit residues: 73.5397 Evaluate side-chains 196 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 291 VAL Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 609 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 666 ASN Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain U residue 801 LYS Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 291 GLU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12846 Z= 0.150 Angle : 0.449 5.581 17413 Z= 0.234 Chirality : 0.042 0.140 1926 Planarity : 0.004 0.039 2229 Dihedral : 8.265 169.304 1735 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 2.09 % Allowed : 13.25 % Favored : 84.67 % 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: 1.24 (0.22), residues: 1541 helix: 1.44 (0.20), residues: 690 sheet: 0.84 (0.36), residues: 215 loop : 0.26 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 356 HIS 0.004 0.001 HIS U 823 PHE 0.012 0.001 PHE U 584 TYR 0.017 0.001 TYR W 319 ARG 0.003 0.000 ARG U 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.450 Fit side-chains REVERT: G 457 MET cc_start: 0.5932 (tpt) cc_final: 0.5664 (tpt) REVERT: G 524 GLN cc_start: 0.6605 (mt0) cc_final: 0.6340 (mt0) REVERT: G 545 LYS cc_start: 0.7868 (mttt) cc_final: 0.7566 (tptt) REVERT: U 286 ASP cc_start: 0.7970 (m-30) cc_final: 0.7601 (t70) REVERT: U 375 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7772 (mt-10) REVERT: U 441 LYS cc_start: 0.7838 (mttt) cc_final: 0.7603 (mmtm) REVERT: U 515 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7437 (mm-30) REVERT: U 574 ASP cc_start: 0.8120 (p0) cc_final: 0.7809 (p0) REVERT: U 688 LYS cc_start: 0.7423 (mttt) cc_final: 0.6967 (pttm) REVERT: U 765 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7605 (mp10) REVERT: U 801 LYS cc_start: 0.8179 (tttt) cc_final: 0.7837 (mttp) REVERT: U 835 ASP cc_start: 0.8593 (m-30) cc_final: 0.8252 (t0) REVERT: U 853 LYS cc_start: 0.8045 (mttt) cc_final: 0.7699 (mmmt) REVERT: V 25 ASP cc_start: 0.8078 (t0) cc_final: 0.7464 (p0) REVERT: V 68 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7442 (mtp-110) REVERT: V 69 TYR cc_start: 0.8882 (m-80) cc_final: 0.8518 (m-80) REVERT: V 160 THR cc_start: 0.9183 (m) cc_final: 0.8893 (m) REVERT: V 225 GLN cc_start: 0.7505 (mt0) cc_final: 0.6839 (tp-100) REVERT: V 246 GLN cc_start: 0.6723 (tt0) cc_final: 0.6260 (pt0) REVERT: V 269 LEU cc_start: 0.8251 (mp) cc_final: 0.8050 (mp) REVERT: V 270 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8127 (mt-10) REVERT: V 292 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8054 (mp0) REVERT: V 326 LYS cc_start: 0.8069 (tttt) cc_final: 0.7606 (tmtt) REVERT: W 91 GLN cc_start: 0.7773 (tt0) cc_final: 0.7449 (tp-100) REVERT: W 182 ARG cc_start: 0.8247 (ptt180) cc_final: 0.7996 (ptt90) REVERT: W 196 LYS cc_start: 0.7660 (tttt) cc_final: 0.7281 (ttpt) REVERT: W 210 LYS cc_start: 0.8257 (mttt) cc_final: 0.8044 (mtpt) REVERT: W 222 ASP cc_start: 0.8709 (m-30) cc_final: 0.8508 (m-30) REVERT: W 224 GLU cc_start: 0.8210 (tt0) cc_final: 0.7883 (tp30) REVERT: W 256 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7228 (tm-30) REVERT: W 277 GLU cc_start: 0.8673 (tt0) cc_final: 0.8237 (mp0) REVERT: W 291 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6476 (tp30) REVERT: W 399 ASP cc_start: 0.8728 (m-30) cc_final: 0.8448 (p0) REVERT: W 425 MET cc_start: 0.7184 (tpt) cc_final: 0.6706 (tpt) REVERT: W 430 LYS cc_start: 0.6830 (mttt) cc_final: 0.6459 (mmtt) REVERT: W 481 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7898 (mp0) REVERT: X 51 LYS cc_start: 0.8147 (tttt) cc_final: 0.7895 (ttmm) outliers start: 29 outliers final: 27 residues processed: 193 average time/residue: 0.2656 time to fit residues: 73.4423 Evaluate side-chains 196 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 291 VAL Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 609 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 666 ASN Chi-restraints excluded: chain U residue 669 LEU Chi-restraints excluded: chain U residue 743 ASP Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 291 GLU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 308 ASN Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 ASN ** W 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120004 restraints weight = 15675.717| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.57 r_work: 0.3137 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12846 Z= 0.159 Angle : 0.454 5.660 17413 Z= 0.236 Chirality : 0.042 0.140 1926 Planarity : 0.004 0.038 2229 Dihedral : 8.251 169.470 1735 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 2.23 % Allowed : 13.17 % Favored : 84.59 % 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: 1.22 (0.22), residues: 1541 helix: 1.44 (0.20), residues: 690 sheet: 0.76 (0.36), residues: 209 loop : 0.25 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 356 HIS 0.004 0.001 HIS U 823 PHE 0.012 0.001 PHE U 584 TYR 0.022 0.001 TYR W 319 ARG 0.002 0.000 ARG V 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.68 seconds wall clock time: 52 minutes 11.31 seconds (3131.31 seconds total)