Starting phenix.real_space_refine (version: dev) on Mon Feb 20 16:57:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2023/8a5o_15179_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2023/8a5o_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_2023/8a5o_15179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2023/8a5o_15179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2023/8a5o_15179_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5o_15179/02_2023/8a5o_15179_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 6.98, per 1000 atoms: 0.56 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: 4.78 Conformation dependent library (CDL) restraints added in 1.9 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: 1.51 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: 3.62 Time building geometry restraints manager: 5.18 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: 7473 27.03 - 54.07: 246 54.07 - 81.10: 37 81.10 - 108.13: 3 108.13 - 135.17: 1 Dihedral angle restraints: 7760 sinusoidal: 3206 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 7757 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 4.370 Check model and map are aligned: 0.160 Process input model: 33.220 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 14.049 135.168 4806 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 % 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 *********************** 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 : 1.670 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 297 average time/residue: 0.2985 time to fit residues: 121.4207 Evaluate side-chains 184 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1135 time to fit residues: 3.2027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 G 524 GLN U 272 HIS U 287 HIS U 324 ASN U 369 ASN U 502 ASN U 799 GLN V 78 ASN V 115 ASN W 95 GLN X 45 ASN X 59 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2326 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= 0.201 Angle : 0.602 8.053 17413 Z= 0.321 Chirality : 0.045 0.146 1926 Planarity : 0.004 0.039 2229 Dihedral : 7.934 139.030 1702 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer Outliers : 1.73 % 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: 0.60 (0.21), residues: 1541 helix: 0.53 (0.19), residues: 695 sheet: 1.05 (0.36), residues: 210 loop : 0.21 (0.25), residues: 636 *********************** 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 221 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 1.642 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 213 average time/residue: 0.2592 time to fit residues: 80.0458 Evaluate side-chains 174 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.556 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1195 time to fit residues: 4.9901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN V 173 HIS W 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12846 Z= 0.263 Angle : 0.563 5.865 17413 Z= 0.295 Chirality : 0.045 0.160 1926 Planarity : 0.004 0.045 2229 Dihedral : 7.840 145.735 1702 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.40 % Rotamer Outliers : 1.01 % 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: 0.77 (0.21), residues: 1541 helix: 0.78 (0.19), residues: 697 sheet: 0.77 (0.35), residues: 214 loop : 0.29 (0.25), residues: 630 *********************** 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 183 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 1.505 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 178 average time/residue: 0.2819 time to fit residues: 71.7875 Evaluate side-chains 156 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1214 time to fit residues: 3.8769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 792 ASN V 225 GLN W 95 GLN W 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 12846 Z= 0.248 Angle : 0.536 7.645 17413 Z= 0.278 Chirality : 0.044 0.143 1926 Planarity : 0.004 0.047 2229 Dihedral : 7.828 150.928 1702 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer Outliers : 1.15 % 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: 0.74 (0.21), residues: 1541 helix: 0.83 (0.19), residues: 699 sheet: 0.78 (0.36), residues: 211 loop : 0.19 (0.25), residues: 631 *********************** 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 173 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.608 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 169 average time/residue: 0.2639 time to fit residues: 64.9914 Evaluate side-chains 150 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1285 time to fit residues: 3.9802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 95 GLN W 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 12846 Z= 0.208 Angle : 0.501 6.105 17413 Z= 0.262 Chirality : 0.043 0.143 1926 Planarity : 0.004 0.044 2229 Dihedral : 7.750 154.084 1702 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer Outliers : 0.86 % 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: 0.78 (0.21), residues: 1541 helix: 0.93 (0.20), residues: 698 sheet: 0.74 (0.36), residues: 205 loop : 0.13 (0.25), residues: 638 *********************** 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 174 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.680 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 171 average time/residue: 0.2776 time to fit residues: 68.4388 Evaluate side-chains 147 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1200 time to fit residues: 3.7493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN W 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3290 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 : 0.543 6.374 17413 Z= 0.280 Chirality : 0.045 0.144 1926 Planarity : 0.004 0.043 2229 Dihedral : 7.957 160.281 1702 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1541 helix: 0.81 (0.19), residues: 697 sheet: 0.66 (0.36), residues: 207 loop : 0.06 (0.25), residues: 637 *********************** 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 165 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.416 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 160 average time/residue: 0.2776 time to fit residues: 63.8869 Evaluate side-chains 154 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1224 time to fit residues: 4.8994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 818 GLN U 821 ASN W 429 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3416 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= 0.142 Angle : 0.460 5.640 17413 Z= 0.241 Chirality : 0.042 0.139 1926 Planarity : 0.004 0.042 2229 Dihedral : 7.746 164.287 1702 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer Outliers : 0.50 % 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: 0.89 (0.22), residues: 1541 helix: 1.11 (0.20), residues: 694 sheet: 0.73 (0.37), residues: 196 loop : 0.11 (0.25), residues: 651 *********************** 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 169 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 1.535 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 168 average time/residue: 0.2630 time to fit residues: 63.9138 Evaluate side-chains 148 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1205 time to fit residues: 3.1507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12846 Z= 0.171 Angle : 0.471 5.416 17413 Z= 0.245 Chirality : 0.042 0.137 1926 Planarity : 0.004 0.041 2229 Dihedral : 7.682 166.240 1702 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.14 % Favored : 97.79 % Rotamer Outliers : 0.36 % 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: 0.96 (0.22), residues: 1541 helix: 1.15 (0.20), residues: 699 sheet: 0.80 (0.37), residues: 209 loop : 0.15 (0.25), residues: 633 *********************** 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 153 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.542 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 151 average time/residue: 0.2715 time to fit residues: 59.6145 Evaluate side-chains 146 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.447 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1954 time to fit residues: 3.7183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 0.0670 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 12846 Z= 0.147 Angle : 0.455 5.386 17413 Z= 0.237 Chirality : 0.042 0.139 1926 Planarity : 0.004 0.039 2229 Dihedral : 7.602 169.396 1702 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.14 % Favored : 97.79 % Rotamer Outliers : 0.22 % 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: 1.31 (0.20), residues: 689 sheet: 0.89 (0.36), residues: 208 loop : 0.19 (0.25), residues: 644 *********************** 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 150 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.614 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 148 average time/residue: 0.2929 time to fit residues: 63.5131 Evaluate side-chains 141 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1157 time to fit residues: 2.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12846 Z= 0.151 Angle : 0.467 5.428 17413 Z= 0.244 Chirality : 0.042 0.190 1926 Planarity : 0.004 0.039 2229 Dihedral : 7.580 171.423 1702 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer Outliers : 0.14 % 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: 1.12 (0.22), residues: 1541 helix: 1.31 (0.20), residues: 688 sheet: 0.90 (0.37), residues: 209 loop : 0.20 (0.25), residues: 644 ********************** 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 149 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.491 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 148 average time/residue: 0.2744 time to fit residues: 59.1196 Evaluate side-chains 146 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1171 time to fit residues: 2.2695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118240 restraints weight = 15671.676| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.64 r_work: 0.3177 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12846 Z= 0.182 Angle : 0.484 9.106 17413 Z= 0.252 Chirality : 0.043 0.270 1926 Planarity : 0.004 0.038 2229 Dihedral : 7.649 174.667 1702 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer Outliers : 0.14 % 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: 1.08 (0.22), residues: 1541 helix: 1.27 (0.20), residues: 689 sheet: 0.92 (0.36), residues: 208 loop : 0.17 (0.25), residues: 644 =============================================================================== Job complete usr+sys time: 2631.16 seconds wall clock time: 48 minutes 39.16 seconds (2919.16 seconds total)