Starting phenix.real_space_refine on Tue Aug 6 06:14:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/08_2024/8z8x_39850.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/08_2024/8z8x_39850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/08_2024/8z8x_39850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/08_2024/8z8x_39850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/08_2024/8z8x_39850.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/08_2024/8z8x_39850.cif" } resolution = 3.06 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 Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 82 5.16 5 C 9238 2.51 5 N 2559 2.21 5 O 2853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ASP 21": "OD1" <-> "OD2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 587": "OD1" <-> "OD2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14768 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5014 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 588} Chain: "B" Number of atoms: 5710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5710 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 39, 'TRANS': 670} Chain: "C" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3253 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 400, 3253 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 3317 Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AILE C 330 " occ=0.68 ... (14 atoms not shown) pdb=" CD1BILE C 330 " occ=0.32 residue: pdb=" N ASER C 336 " occ=0.72 ... (10 atoms not shown) pdb=" OG BSER C 336 " occ=0.28 residue: pdb=" N ASER C 384 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER C 384 " occ=0.44 Time building chain proxies: 9.83, per 1000 atoms: 0.67 Number of scatterers: 14768 At special positions: 0 Unit cell: (108.714, 105.12, 138.363, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 36 15.00 O 2853 8.00 N 2559 7.00 C 9238 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: 5.97 Conformation dependent library (CDL) restraints added in 2.9 seconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 21 sheets defined 46.5% alpha, 11.8% beta 8 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 155 removed outlier: 3.529A pdb=" N TRP A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.830A pdb=" N VAL A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.515A pdb=" N LEU A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.722A pdb=" N TRP A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.542A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.693A pdb=" N GLU A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 removed outlier: 4.354A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.368A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.686A pdb=" N THR A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.651A pdb=" N ASN A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.465A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.502A pdb=" N GLU A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'B' and resid 11 through 20 removed outlier: 4.310A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.552A pdb=" N GLY B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.737A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.873A pdb=" N GLU B 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.933A pdb=" N LYS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.920A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.682A pdb=" N MET B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.701A pdb=" N VAL B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 432 through 450 removed outlier: 3.568A pdb=" N VAL B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.904A pdb=" N CYS B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 551 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 568 through 572 removed outlier: 4.005A pdb=" N MET B 572 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.599A pdb=" N ARG B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 662 removed outlier: 4.205A pdb=" N ASN B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 695 Processing helix chain 'B' and resid 698 through 709 Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.284A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 52 through 55 removed outlier: 3.840A pdb=" N MET C 55 " --> pdb=" O ALA C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 102 through 110 removed outlier: 3.871A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.932A pdb=" N HIS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.755A pdb=" N CYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 413 removed outlier: 3.591A pdb=" N LEU C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 447 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.670A pdb=" N PHE A 119 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.674A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242 removed outlier: 5.566A pdb=" N PHE A 425 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 416 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 427 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.954A pdb=" N LEU B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 530 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 191 removed outlier: 4.894A pdb=" N GLN B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 242 through 246 removed outlier: 7.450A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 467 through 470 removed outlier: 4.418A pdb=" N PHE B 474 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 608 through 611 removed outlier: 3.701A pdb=" N MET B 609 " --> pdb=" O MET B 621 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 67 through 69 removed outlier: 5.041A pdb=" N ARG C 98 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 143 Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 154 Processing sheet with id=AC2, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.539A pdb=" N ASN C 339 " --> pdb=" O LYS C 371 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 394 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU C 392 " --> pdb=" O ASER C 384 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 386 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR C 482 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 393 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 345 through 352 625 hydrogen bonds defined for protein. 1723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4723 1.34 - 1.47: 3681 1.47 - 1.60: 6603 1.60 - 1.72: 36 1.72 - 1.85: 135 Bond restraints: 15178 Sorted by residual: bond pdb=" N GLY C 455 " pdb=" CA GLY C 455 " ideal model delta sigma weight residual 1.449 1.471 -0.021 1.45e-02 4.76e+03 2.20e+00 bond pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.34e+00 bond pdb=" CG1 ILE A 393 " pdb=" CD1 ILE A 393 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.27e+00 bond pdb=" CB PRO B 644 " pdb=" CG PRO B 644 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.12e+00 bond pdb=" CB GLU B 263 " pdb=" CG GLU B 263 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 ... (remaining 15173 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.73: 591 105.73 - 112.84: 8049 112.84 - 119.95: 5329 119.95 - 127.06: 6484 127.06 - 134.17: 269 Bond angle restraints: 20722 Sorted by residual: angle pdb=" C ARG C 62 " pdb=" N LYS C 63 " pdb=" CA LYS C 63 " ideal model delta sigma weight residual 120.49 129.87 -9.38 1.42e+00 4.96e-01 4.37e+01 angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 113.53 107.59 5.94 9.80e-01 1.04e+00 3.68e+01 angle pdb=" C VAL C 102 " pdb=" N VAL C 103 " pdb=" CA VAL C 103 " ideal model delta sigma weight residual 120.24 122.76 -2.52 6.30e-01 2.52e+00 1.60e+01 angle pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sigma weight residual 120.20 125.12 -4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" N VAL A 597 " pdb=" CA VAL A 597 " pdb=" C VAL A 597 " ideal model delta sigma weight residual 111.81 109.14 2.67 8.60e-01 1.35e+00 9.67e+00 ... (remaining 20717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 9066 33.81 - 67.61: 229 67.61 - 101.42: 26 101.42 - 135.22: 1 135.22 - 169.03: 2 Dihedral angle restraints: 9324 sinusoidal: 4228 harmonic: 5096 Sorted by residual: dihedral pdb=" CA GLU A 456 " pdb=" C GLU A 456 " pdb=" N GLU A 457 " pdb=" CA GLU A 457 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sinusoidal sigma weight residual -110.00 59.03 -169.03 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' C E 7 " pdb=" C3' C E 7 " pdb=" O3' C E 7 " pdb=" P U E 8 " ideal model delta sinusoidal sigma weight residual 220.00 69.54 150.46 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1611 0.037 - 0.074: 496 0.074 - 0.111: 167 0.111 - 0.148: 37 0.148 - 0.185: 2 Chirality restraints: 2313 Sorted by residual: chirality pdb=" C3' A E 2 " pdb=" C4' A E 2 " pdb=" O3' A E 2 " pdb=" C2' A E 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA GLU B 263 " pdb=" N GLU B 263 " pdb=" C GLU B 263 " pdb=" CB GLU B 263 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE C 395 " pdb=" N ILE C 395 " pdb=" C ILE C 395 " pdb=" CB ILE C 395 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 2310 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 643 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 644 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 464 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 354 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO C 355 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 355 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 355 " -0.034 5.00e-02 4.00e+02 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 427 2.70 - 3.25: 14967 3.25 - 3.80: 23895 3.80 - 4.35: 32670 4.35 - 4.90: 52933 Nonbonded interactions: 124892 Sorted by model distance: nonbonded pdb=" OE1 GLU A 126 " pdb=" OG SER A 128 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR C 229 " pdb=" O VAL C 231 " model vdw 2.158 3.040 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.184 3.040 nonbonded pdb=" OE1 GLU C 10 " pdb=" OG1 THR C 12 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN B 132 " pdb=" ND2 ASN B 227 " model vdw 2.264 3.120 ... (remaining 124887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.28 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 45.400 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15178 Z= 0.175 Angle : 0.610 9.385 20722 Z= 0.328 Chirality : 0.041 0.185 2313 Planarity : 0.006 0.083 2532 Dihedral : 14.960 169.029 6016 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.67 (0.20), residues: 1729 helix: 0.66 (0.20), residues: 715 sheet: -0.83 (0.37), residues: 207 loop : -1.33 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 185 HIS 0.003 0.001 HIS C 242 PHE 0.024 0.002 PHE C 335 TYR 0.010 0.001 TYR B 533 ARG 0.008 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8841 (m-30) cc_final: 0.8636 (m-30) REVERT: A 150 GLU cc_start: 0.8924 (mp0) cc_final: 0.8692 (pm20) REVERT: B 259 ASP cc_start: 0.8364 (m-30) cc_final: 0.8147 (m-30) REVERT: C 380 GLN cc_start: 0.8244 (pm20) cc_final: 0.7997 (pm20) REVERT: C 383 PHE cc_start: 0.8549 (p90) cc_final: 0.8223 (p90) REVERT: C 410 ILE cc_start: 0.8952 (mt) cc_final: 0.8511 (mt) REVERT: C 421 PHE cc_start: 0.7675 (m-80) cc_final: 0.7413 (m-80) REVERT: C 433 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7538 (tpp80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3078 time to fit residues: 105.0049 Evaluate side-chains 199 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 257 GLN B 123 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15178 Z= 0.314 Angle : 0.637 6.627 20722 Z= 0.330 Chirality : 0.045 0.180 2313 Planarity : 0.005 0.062 2532 Dihedral : 13.499 164.876 2463 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.09 % Allowed : 7.69 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.55 (0.20), residues: 1729 helix: 0.86 (0.20), residues: 718 sheet: -1.05 (0.34), residues: 226 loop : -1.30 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.011 0.001 HIS C 233 PHE 0.028 0.002 PHE C 41 TYR 0.034 0.002 TYR C 382 ARG 0.006 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: B 259 ASP cc_start: 0.8487 (m-30) cc_final: 0.8211 (m-30) REVERT: C 110 TYR cc_start: 0.8273 (m-80) cc_final: 0.8035 (m-80) REVERT: C 346 GLU cc_start: 0.9006 (tt0) cc_final: 0.8322 (tm-30) REVERT: C 380 GLN cc_start: 0.8556 (pm20) cc_final: 0.8269 (pm20) REVERT: C 383 PHE cc_start: 0.8454 (p90) cc_final: 0.8139 (p90) REVERT: C 410 ILE cc_start: 0.8849 (mt) cc_final: 0.8568 (mt) REVERT: C 416 PHE cc_start: 0.8463 (m-80) cc_final: 0.8117 (m-10) REVERT: C 433 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7576 (tpp80) outliers start: 17 outliers final: 10 residues processed: 214 average time/residue: 0.3261 time to fit residues: 97.0589 Evaluate side-chains 196 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN C 233 HIS ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 GLN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15178 Z= 0.177 Angle : 0.562 6.994 20722 Z= 0.288 Chirality : 0.041 0.172 2313 Planarity : 0.005 0.053 2532 Dihedral : 13.372 163.971 2463 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.03 % Allowed : 10.13 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.35 (0.20), residues: 1729 helix: 1.07 (0.20), residues: 713 sheet: -0.96 (0.34), residues: 225 loop : -1.22 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.006 0.001 HIS C 443 PHE 0.026 0.002 PHE C 41 TYR 0.021 0.001 TYR C 373 ARG 0.005 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 1.557 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8673 (m-30) cc_final: 0.8410 (p0) REVERT: A 159 GLN cc_start: 0.9041 (tp40) cc_final: 0.8730 (tp-100) REVERT: B 259 ASP cc_start: 0.8478 (m-30) cc_final: 0.8171 (m-30) REVERT: B 473 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7565 (mtmm) REVERT: C 110 TYR cc_start: 0.8231 (m-80) cc_final: 0.8007 (m-80) REVERT: C 346 GLU cc_start: 0.8998 (tt0) cc_final: 0.8324 (tm-30) REVERT: C 349 LYS cc_start: 0.7752 (tptp) cc_final: 0.7516 (tptt) REVERT: C 380 GLN cc_start: 0.8549 (pm20) cc_final: 0.8216 (pm20) REVERT: C 423 GLN cc_start: 0.8195 (pm20) cc_final: 0.7915 (pm20) REVERT: C 433 ARG cc_start: 0.8021 (tpp-160) cc_final: 0.7568 (tpp80) outliers start: 16 outliers final: 9 residues processed: 209 average time/residue: 0.3463 time to fit residues: 102.9409 Evaluate side-chains 200 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 30.0000 chunk 169 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN C 233 HIS ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15178 Z= 0.344 Angle : 0.616 7.576 20722 Z= 0.316 Chirality : 0.044 0.193 2313 Planarity : 0.005 0.055 2532 Dihedral : 13.416 164.419 2463 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.41 % Allowed : 10.90 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.52 (0.20), residues: 1729 helix: 0.90 (0.20), residues: 730 sheet: -1.01 (0.34), residues: 228 loop : -1.33 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 253 HIS 0.010 0.001 HIS C 233 PHE 0.027 0.002 PHE C 41 TYR 0.025 0.002 TYR C 382 ARG 0.005 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8665 (m-30) cc_final: 0.8421 (p0) REVERT: A 159 GLN cc_start: 0.9084 (tp40) cc_final: 0.8731 (tp-100) REVERT: A 569 MET cc_start: 0.8712 (tpp) cc_final: 0.8432 (tpt) REVERT: B 186 ASP cc_start: 0.8748 (t70) cc_final: 0.8391 (t0) REVERT: B 255 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8344 (tttp) REVERT: B 259 ASP cc_start: 0.8502 (m-30) cc_final: 0.8141 (m-30) REVERT: B 473 LYS cc_start: 0.7963 (mmmt) cc_final: 0.7587 (mtmm) REVERT: C 346 GLU cc_start: 0.9003 (tt0) cc_final: 0.8365 (tm-30) REVERT: C 374 PHE cc_start: 0.8518 (p90) cc_final: 0.8249 (p90) REVERT: C 380 GLN cc_start: 0.8567 (pm20) cc_final: 0.8216 (pm20) REVERT: C 423 GLN cc_start: 0.8301 (pm20) cc_final: 0.7998 (pm20) REVERT: C 433 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7574 (tpp80) outliers start: 22 outliers final: 18 residues processed: 206 average time/residue: 0.3114 time to fit residues: 90.5827 Evaluate side-chains 197 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15178 Z= 0.193 Angle : 0.557 7.204 20722 Z= 0.285 Chirality : 0.041 0.178 2313 Planarity : 0.005 0.054 2532 Dihedral : 13.309 163.434 2463 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.54 % Allowed : 10.90 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.34 (0.20), residues: 1729 helix: 1.07 (0.20), residues: 725 sheet: -0.98 (0.34), residues: 228 loop : -1.23 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 253 HIS 0.007 0.001 HIS C 233 PHE 0.026 0.001 PHE C 41 TYR 0.016 0.001 TYR B 533 ARG 0.006 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 GLN cc_start: 0.9105 (tp40) cc_final: 0.8747 (tp-100) REVERT: B 255 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8418 (ttmm) REVERT: B 259 ASP cc_start: 0.8516 (m-30) cc_final: 0.8281 (m-30) REVERT: B 473 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7584 (mtmm) REVERT: C 18 GLU cc_start: 0.7060 (tp30) cc_final: 0.6830 (tp30) REVERT: C 160 GLU cc_start: 0.8092 (tp30) cc_final: 0.7865 (tp30) REVERT: C 346 GLU cc_start: 0.8959 (tt0) cc_final: 0.8431 (tm-30) REVERT: C 374 PHE cc_start: 0.8382 (p90) cc_final: 0.8116 (p90) REVERT: C 380 GLN cc_start: 0.8576 (pm20) cc_final: 0.8210 (pm20) REVERT: C 416 PHE cc_start: 0.8286 (m-80) cc_final: 0.7840 (m-10) REVERT: C 423 GLN cc_start: 0.8416 (pm20) cc_final: 0.8087 (pm20) REVERT: C 437 ASP cc_start: 0.8807 (m-30) cc_final: 0.8526 (m-30) outliers start: 24 outliers final: 17 residues processed: 211 average time/residue: 0.3310 time to fit residues: 99.0762 Evaluate side-chains 204 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 33 optimal weight: 0.0570 chunk 99 optimal weight: 0.0170 chunk 41 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 88 optimal weight: 0.0020 chunk 163 optimal weight: 4.9990 overall best weight: 1.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN C 254 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15178 Z= 0.177 Angle : 0.553 7.099 20722 Z= 0.282 Chirality : 0.041 0.174 2313 Planarity : 0.005 0.054 2532 Dihedral : 13.254 163.127 2463 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 11.22 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1729 helix: 1.20 (0.20), residues: 716 sheet: -0.89 (0.34), residues: 228 loop : -1.18 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.006 0.001 HIS C 233 PHE 0.025 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.006 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8672 (m-30) cc_final: 0.8428 (p0) REVERT: A 159 GLN cc_start: 0.9118 (tp40) cc_final: 0.8731 (tp-100) REVERT: B 186 ASP cc_start: 0.8734 (t70) cc_final: 0.8360 (t0) REVERT: B 259 ASP cc_start: 0.8565 (m-30) cc_final: 0.8267 (m-30) REVERT: B 473 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7589 (mtmm) REVERT: C 29 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8727 (ttpp) REVERT: C 160 GLU cc_start: 0.8082 (tp30) cc_final: 0.7864 (tp30) REVERT: C 346 GLU cc_start: 0.8933 (tt0) cc_final: 0.8434 (tm-30) REVERT: C 349 LYS cc_start: 0.7728 (tptt) cc_final: 0.7495 (tptp) REVERT: C 374 PHE cc_start: 0.8465 (p90) cc_final: 0.8257 (p90) REVERT: C 380 GLN cc_start: 0.8572 (pm20) cc_final: 0.8190 (pm20) outliers start: 27 outliers final: 19 residues processed: 215 average time/residue: 0.3136 time to fit residues: 95.7423 Evaluate side-chains 202 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 0.0870 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN B 148 GLN C 233 HIS C 254 ASN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15178 Z= 0.153 Angle : 0.559 8.037 20722 Z= 0.284 Chirality : 0.041 0.195 2313 Planarity : 0.005 0.056 2532 Dihedral : 13.223 162.634 2463 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.47 % Allowed : 12.44 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1729 helix: 1.26 (0.20), residues: 715 sheet: -0.82 (0.34), residues: 226 loop : -1.13 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 253 HIS 0.009 0.001 HIS C 233 PHE 0.024 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.007 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9024 (mtp180) cc_final: 0.8821 (mtp180) REVERT: A 140 ASP cc_start: 0.8675 (m-30) cc_final: 0.8426 (p0) REVERT: A 159 GLN cc_start: 0.9126 (tp40) cc_final: 0.8732 (tp-100) REVERT: B 259 ASP cc_start: 0.8550 (m-30) cc_final: 0.8274 (m-30) REVERT: B 473 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7571 (mtmm) REVERT: C 95 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7741 (ptmm) REVERT: C 160 GLU cc_start: 0.8064 (tp30) cc_final: 0.7818 (tp30) REVERT: C 346 GLU cc_start: 0.8940 (tt0) cc_final: 0.8462 (tm-30) REVERT: C 349 LYS cc_start: 0.7700 (tptt) cc_final: 0.7445 (tptp) REVERT: C 374 PHE cc_start: 0.8441 (p90) cc_final: 0.8225 (p90) REVERT: C 380 GLN cc_start: 0.8575 (pm20) cc_final: 0.8192 (pm20) outliers start: 23 outliers final: 22 residues processed: 207 average time/residue: 0.3155 time to fit residues: 92.1755 Evaluate side-chains 210 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 408 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 257 GLN C 233 HIS ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15178 Z= 0.204 Angle : 0.570 7.585 20722 Z= 0.290 Chirality : 0.041 0.184 2313 Planarity : 0.005 0.056 2532 Dihedral : 13.225 162.804 2463 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.86 % Allowed : 12.37 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.12 (0.20), residues: 1729 helix: 1.24 (0.20), residues: 719 sheet: -0.74 (0.34), residues: 225 loop : -1.12 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.011 0.001 HIS C 233 PHE 0.025 0.001 PHE C 41 TYR 0.016 0.001 TYR B 533 ARG 0.007 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9027 (mtp180) cc_final: 0.8825 (mtp180) REVERT: A 140 ASP cc_start: 0.8662 (m-30) cc_final: 0.8429 (p0) REVERT: A 159 GLN cc_start: 0.9123 (tp40) cc_final: 0.8730 (tp-100) REVERT: B 186 ASP cc_start: 0.8750 (t70) cc_final: 0.8371 (t0) REVERT: B 259 ASP cc_start: 0.8565 (m-30) cc_final: 0.8262 (m-30) REVERT: B 302 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7249 (mm-40) REVERT: B 473 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7613 (mtmm) REVERT: B 701 ARG cc_start: 0.9250 (mtp85) cc_final: 0.9038 (mtp85) REVERT: C 18 GLU cc_start: 0.6988 (tp30) cc_final: 0.6779 (tp30) REVERT: C 95 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7753 (ptmm) REVERT: C 160 GLU cc_start: 0.8080 (tp30) cc_final: 0.7830 (tp30) REVERT: C 346 GLU cc_start: 0.8945 (tt0) cc_final: 0.8457 (tm-30) REVERT: C 380 GLN cc_start: 0.8585 (pm20) cc_final: 0.8203 (pm20) outliers start: 29 outliers final: 23 residues processed: 206 average time/residue: 0.3181 time to fit residues: 92.5243 Evaluate side-chains 206 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 408 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 30.0000 chunk 147 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN C 233 HIS ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15178 Z= 0.343 Angle : 0.630 8.764 20722 Z= 0.322 Chirality : 0.044 0.271 2313 Planarity : 0.005 0.055 2532 Dihedral : 13.356 163.970 2463 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.79 % Allowed : 12.31 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1729 helix: 1.15 (0.20), residues: 722 sheet: -0.73 (0.34), residues: 226 loop : -1.19 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 470 HIS 0.006 0.001 HIS C 233 PHE 0.026 0.002 PHE C 41 TYR 0.018 0.002 TYR B 537 ARG 0.007 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8675 (m-30) cc_final: 0.8438 (p0) REVERT: A 159 GLN cc_start: 0.9129 (tp40) cc_final: 0.8735 (tp-100) REVERT: A 569 MET cc_start: 0.8709 (tpp) cc_final: 0.8448 (tpt) REVERT: B 255 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8303 (tttp) REVERT: B 259 ASP cc_start: 0.8556 (m-30) cc_final: 0.8252 (m-30) REVERT: B 302 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7239 (mm-40) REVERT: B 473 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7602 (mtmm) REVERT: C 346 GLU cc_start: 0.8960 (tt0) cc_final: 0.8483 (tm-30) REVERT: C 349 LYS cc_start: 0.7467 (tptt) cc_final: 0.7201 (tptp) REVERT: C 380 GLN cc_start: 0.8640 (pm20) cc_final: 0.8262 (pm20) outliers start: 28 outliers final: 22 residues processed: 206 average time/residue: 0.3193 time to fit residues: 92.4994 Evaluate side-chains 199 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.0570 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 257 GLN C 233 HIS ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15178 Z= 0.156 Angle : 0.580 7.641 20722 Z= 0.295 Chirality : 0.041 0.208 2313 Planarity : 0.005 0.056 2532 Dihedral : 13.231 162.702 2463 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.47 % Allowed : 12.95 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.11 (0.20), residues: 1729 helix: 1.25 (0.20), residues: 719 sheet: -0.72 (0.34), residues: 222 loop : -1.12 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 230 HIS 0.010 0.001 HIS C 233 PHE 0.030 0.001 PHE C 383 TYR 0.016 0.001 TYR B 533 ARG 0.008 0.000 ARG B 477 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8659 (m-30) cc_final: 0.8417 (p0) REVERT: A 159 GLN cc_start: 0.9120 (tp40) cc_final: 0.8674 (tp-100) REVERT: B 120 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8734 (mtmt) REVERT: B 186 ASP cc_start: 0.8737 (t70) cc_final: 0.8404 (t0) REVERT: B 248 MET cc_start: 0.8917 (tpp) cc_final: 0.8715 (tpt) REVERT: B 259 ASP cc_start: 0.8557 (m-30) cc_final: 0.8277 (m-30) REVERT: B 302 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7251 (mm-40) REVERT: B 473 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7575 (mtmm) REVERT: C 95 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7740 (ptmm) REVERT: C 346 GLU cc_start: 0.8940 (tt0) cc_final: 0.8412 (tm-30) REVERT: C 349 LYS cc_start: 0.7525 (tptt) cc_final: 0.7286 (tptp) REVERT: C 380 GLN cc_start: 0.8600 (pm20) cc_final: 0.8216 (pm20) outliers start: 23 outliers final: 19 residues processed: 205 average time/residue: 0.3226 time to fit residues: 92.7869 Evaluate side-chains 204 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN C 233 HIS ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.084364 restraints weight = 58774.999| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.86 r_work: 0.2822 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15178 Z= 0.165 Angle : 0.575 7.915 20722 Z= 0.291 Chirality : 0.041 0.173 2313 Planarity : 0.005 0.055 2532 Dihedral : 13.203 162.648 2463 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.41 % Allowed : 13.08 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.03 (0.20), residues: 1729 helix: 1.33 (0.20), residues: 719 sheet: -0.66 (0.34), residues: 222 loop : -1.09 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 185 HIS 0.012 0.001 HIS C 233 PHE 0.026 0.001 PHE C 383 TYR 0.015 0.001 TYR B 533 ARG 0.007 0.000 ARG B 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.41 seconds wall clock time: 59 minutes 27.40 seconds (3567.40 seconds total)