Starting phenix.real_space_refine on Wed Mar 20 16:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nha_12322/03_2024/7nha_12322.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nha_12322/03_2024/7nha_12322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nha_12322/03_2024/7nha_12322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nha_12322/03_2024/7nha_12322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nha_12322/03_2024/7nha_12322.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nha_12322/03_2024/7nha_12322.pdb" } resolution = 2.91 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= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 102 5.16 5 C 8854 2.51 5 N 2468 2.21 5 O 2734 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ASP 479": "OD1" <-> "OD2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 729": "OD1" <-> "OD2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C GLU 192": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28049 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 11704 Classifications: {'peptide': 735} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4075 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 12.89, per 1000 atoms: 0.46 Number of scatterers: 28049 At special positions: 0 Unit cell: (99, 103.95, 146.025, 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 102 16.00 P 23 15.00 O 2734 8.00 N 2468 7.00 C 8854 6.00 H 13868 1.00 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: 26.00 Conformation dependent library (CDL) restraints added in 3.4 seconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 15 sheets defined 52.1% alpha, 12.6% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 14.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.006A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.691A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.635A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.777A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.826A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.588A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.331A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.978A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.619A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.517A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.634A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 692 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 11.69 Time building geometry restraints manager: 26.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13841 1.03 - 1.23: 76 1.23 - 1.43: 6041 1.43 - 1.62: 8251 1.62 - 1.82: 177 Bond restraints: 28386 Sorted by residual: bond pdb=" C GLU A 677 " pdb=" O GLU A 677 " ideal model delta sigma weight residual 1.235 1.223 0.012 4.70e-03 4.53e+04 6.23e+00 bond pdb=" CE1 PHE B 730 " pdb=" CZ PHE B 730 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CA PRO A 274 " pdb=" C PRO A 274 " ideal model delta sigma weight residual 1.514 1.520 -0.006 5.50e-03 3.31e+04 1.25e+00 bond pdb=" CG GLU C 6 " pdb=" CD GLU C 6 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" C LEU A 106 " pdb=" N PRO A 107 " ideal model delta sigma weight residual 1.326 1.340 -0.014 1.44e-02 4.82e+03 9.51e-01 ... (remaining 28381 not shown) Histogram of bond angle deviations from ideal: 79.78 - 91.57: 4 91.57 - 103.37: 203 103.37 - 115.16: 35980 115.16 - 126.96: 14861 126.96 - 138.75: 232 Bond angle restraints: 51280 Sorted by residual: angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 108.00 79.78 28.22 3.00e+00 1.11e-01 8.85e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.33 27.67 3.00e+00 1.11e-01 8.51e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.85 27.15 3.00e+00 1.11e-01 8.19e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.45 26.55 3.00e+00 1.11e-01 7.83e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.75 -26.85 3.20e+00 9.77e-02 7.04e+01 ... (remaining 51275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12171 17.93 - 35.86: 828 35.86 - 53.79: 248 53.79 - 71.72: 84 71.72 - 89.65: 15 Dihedral angle restraints: 13346 sinusoidal: 7560 harmonic: 5786 Sorted by residual: dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual 180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP B 729 " pdb=" C ASP B 729 " pdb=" N PHE B 730 " pdb=" CA PHE B 730 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 13343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1598 0.037 - 0.074: 430 0.074 - 0.111: 101 0.111 - 0.148: 31 0.148 - 0.185: 2 Chirality restraints: 2162 Sorted by residual: chirality pdb=" CA PHE B 730 " pdb=" N PHE B 730 " pdb=" C PHE B 730 " pdb=" CB PHE B 730 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE B 302 " pdb=" N ILE B 302 " pdb=" C ILE B 302 " pdb=" CB ILE B 302 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 2159 not shown) Planarity restraints: 4097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 446 " -0.019 2.00e-02 2.50e+03 1.57e-02 7.42e+00 pdb=" CG PHE A 446 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 446 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 446 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 446 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 446 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 446 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 446 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 446 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 446 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 446 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 446 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 730 " 0.015 2.00e-02 2.50e+03 1.17e-02 4.08e+00 pdb=" CG PHE B 730 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 730 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 730 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 730 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE B 730 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 730 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE B 730 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 730 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 730 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 730 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 730 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " -0.016 2.00e-02 2.50e+03 1.16e-02 4.05e+00 pdb=" CG PHE A 46 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 46 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 46 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 46 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 46 " 0.001 2.00e-02 2.50e+03 ... (remaining 4094 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1258 2.17 - 2.78: 56096 2.78 - 3.39: 80157 3.39 - 3.99: 104338 3.99 - 4.60: 163228 Nonbonded interactions: 405077 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.566 1.850 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.569 1.850 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 1.850 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 1.850 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 1.850 ... (remaining 405072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.430 Extract box with map and model: 5.150 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 106.230 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.035 14518 Z= 0.168 Angle : 0.572 26.852 19687 Z= 0.313 Chirality : 0.038 0.185 2162 Planarity : 0.004 0.076 2456 Dihedral : 14.221 89.651 5702 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.71 (0.20), residues: 1692 helix: 0.45 (0.19), residues: 786 sheet: -0.81 (0.42), residues: 143 loop : -1.35 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 88 HIS 0.003 0.001 HIS A 41 PHE 0.048 0.002 PHE A 446 TYR 0.010 0.001 TYR A 24 ARG 0.007 0.001 ARG B 727 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8632 (t80) cc_final: 0.8388 (t80) REVERT: A 104 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8628 (tptt) REVERT: A 561 MET cc_start: 0.7246 (tmm) cc_final: 0.6795 (tmm) REVERT: B 743 ILE cc_start: 0.8345 (mm) cc_final: 0.7558 (mp) REVERT: C 9 ASP cc_start: 0.8742 (m-30) cc_final: 0.8531 (m-30) REVERT: C 47 MET cc_start: 0.9197 (tpp) cc_final: 0.8966 (tpp) REVERT: C 194 GLN cc_start: 0.7979 (pp30) cc_final: 0.7425 (pp30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 2.8449 time to fit residues: 574.7097 Evaluate side-chains 127 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 HIS B 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14518 Z= 0.290 Angle : 0.591 27.305 19687 Z= 0.307 Chirality : 0.039 0.178 2162 Planarity : 0.004 0.073 2456 Dihedral : 10.251 73.451 2207 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.13 % Allowed : 6.55 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1692 helix: 0.64 (0.19), residues: 790 sheet: -0.93 (0.40), residues: 161 loop : -1.33 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 88 HIS 0.003 0.001 HIS A 41 PHE 0.046 0.002 PHE A 446 TYR 0.013 0.001 TYR A 540 ARG 0.006 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8562 (t80) cc_final: 0.8348 (t80) REVERT: B 744 MET cc_start: 0.8961 (mmm) cc_final: 0.8727 (mmm) REVERT: C 9 ASP cc_start: 0.8800 (m-30) cc_final: 0.8579 (m-30) REVERT: C 194 GLN cc_start: 0.7911 (pp30) cc_final: 0.7675 (pp30) outliers start: 17 outliers final: 6 residues processed: 137 average time/residue: 2.4048 time to fit residues: 368.8199 Evaluate side-chains 130 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 161 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14518 Z= 0.323 Angle : 0.593 27.012 19687 Z= 0.308 Chirality : 0.039 0.140 2162 Planarity : 0.004 0.038 2456 Dihedral : 10.163 73.426 2207 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.13 % Allowed : 7.94 % Favored : 90.93 % 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: -0.51 (0.20), residues: 1692 helix: 0.74 (0.19), residues: 792 sheet: -0.80 (0.40), residues: 166 loop : -1.41 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.011 0.001 HIS B 649 PHE 0.022 0.001 PHE B 730 TYR 0.013 0.001 TYR A 540 ARG 0.004 0.000 ARG B 727 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8579 (t80) cc_final: 0.8317 (t80) REVERT: B 744 MET cc_start: 0.8952 (mmm) cc_final: 0.8709 (mmm) REVERT: C 9 ASP cc_start: 0.8810 (m-30) cc_final: 0.8581 (m-30) REVERT: C 194 GLN cc_start: 0.7974 (pp30) cc_final: 0.7767 (pp30) outliers start: 17 outliers final: 6 residues processed: 135 average time/residue: 2.3662 time to fit residues: 357.5895 Evaluate side-chains 130 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain C residue 146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14518 Z= 0.341 Angle : 0.587 25.982 19687 Z= 0.305 Chirality : 0.039 0.142 2162 Planarity : 0.004 0.036 2456 Dihedral : 10.124 73.641 2207 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.32 % Allowed : 9.00 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1692 helix: 0.82 (0.19), residues: 796 sheet: -0.81 (0.41), residues: 168 loop : -1.48 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.011 0.001 HIS B 649 PHE 0.050 0.002 PHE A 446 TYR 0.012 0.001 TYR A 540 ARG 0.006 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8575 (t80) cc_final: 0.8311 (t80) REVERT: A 88 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.7564 (m-10) REVERT: B 744 MET cc_start: 0.8931 (mmm) cc_final: 0.8681 (mmm) REVERT: C 9 ASP cc_start: 0.8796 (m-30) cc_final: 0.8539 (m-30) outliers start: 20 outliers final: 12 residues processed: 138 average time/residue: 2.3687 time to fit residues: 369.4523 Evaluate side-chains 137 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 161 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 139 optimal weight: 0.0060 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14518 Z= 0.244 Angle : 0.568 27.215 19687 Z= 0.289 Chirality : 0.038 0.148 2162 Planarity : 0.004 0.037 2456 Dihedral : 10.048 73.527 2207 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.99 % Allowed : 10.46 % Favored : 88.55 % 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: -0.35 (0.20), residues: 1692 helix: 0.98 (0.19), residues: 796 sheet: -0.85 (0.39), residues: 170 loop : -1.44 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.003 0.001 HIS A 41 PHE 0.021 0.001 PHE B 730 TYR 0.009 0.001 TYR A 540 ARG 0.003 0.000 ARG B 727 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8588 (t80) cc_final: 0.8256 (t80) REVERT: A 88 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.7542 (m-10) REVERT: B 744 MET cc_start: 0.8938 (mmm) cc_final: 0.8712 (mmm) REVERT: C 9 ASP cc_start: 0.8776 (m-30) cc_final: 0.8525 (m-30) REVERT: C 195 ASP cc_start: 0.8114 (p0) cc_final: 0.7911 (p0) outliers start: 15 outliers final: 11 residues processed: 136 average time/residue: 2.3182 time to fit residues: 353.8972 Evaluate side-chains 135 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain C residue 146 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14518 Z= 0.228 Angle : 0.555 26.637 19687 Z= 0.281 Chirality : 0.037 0.145 2162 Planarity : 0.003 0.036 2456 Dihedral : 9.967 73.499 2207 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.99 % Allowed : 10.85 % Favored : 88.15 % 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: -0.18 (0.20), residues: 1692 helix: 1.16 (0.19), residues: 795 sheet: -0.78 (0.40), residues: 170 loop : -1.41 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.003 0.001 HIS B 649 PHE 0.044 0.001 PHE A 446 TYR 0.011 0.001 TYR A 110 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8573 (t80) cc_final: 0.8234 (t80) REVERT: A 88 TRP cc_start: 0.8144 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: A 180 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8715 (mp-120) REVERT: B 714 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8345 (mtt) REVERT: B 744 MET cc_start: 0.8934 (mmm) cc_final: 0.8723 (mmm) REVERT: C 9 ASP cc_start: 0.8766 (m-30) cc_final: 0.8508 (m-30) outliers start: 15 outliers final: 9 residues processed: 136 average time/residue: 2.3772 time to fit residues: 367.2211 Evaluate side-chains 135 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain C residue 146 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14518 Z= 0.291 Angle : 0.574 26.727 19687 Z= 0.292 Chirality : 0.038 0.143 2162 Planarity : 0.004 0.036 2456 Dihedral : 9.944 73.573 2207 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.86 % Allowed : 11.91 % Favored : 87.23 % 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: -0.19 (0.20), residues: 1692 helix: 1.18 (0.19), residues: 796 sheet: -0.80 (0.40), residues: 170 loop : -1.45 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.003 0.001 HIS B 562 PHE 0.020 0.001 PHE B 730 TYR 0.010 0.001 TYR A 540 ARG 0.003 0.000 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8551 (t80) cc_final: 0.8216 (t80) REVERT: A 88 TRP cc_start: 0.8213 (OUTLIER) cc_final: 0.7593 (m-10) REVERT: B 714 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: C 9 ASP cc_start: 0.8793 (m-30) cc_final: 0.8531 (m-30) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 2.3547 time to fit residues: 343.5325 Evaluate side-chains 132 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain C residue 146 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 128 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14518 Z= 0.213 Angle : 0.557 26.578 19687 Z= 0.279 Chirality : 0.037 0.146 2162 Planarity : 0.003 0.035 2456 Dihedral : 9.891 73.484 2207 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.99 % Allowed : 11.85 % Favored : 87.16 % 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: -0.03 (0.20), residues: 1692 helix: 1.33 (0.19), residues: 796 sheet: -0.70 (0.40), residues: 170 loop : -1.41 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.002 0.001 HIS A 41 PHE 0.049 0.001 PHE A 446 TYR 0.011 0.001 TYR A 110 ARG 0.002 0.000 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8547 (t80) cc_final: 0.8218 (t80) REVERT: A 88 TRP cc_start: 0.8212 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: A 637 CYS cc_start: 0.7730 (m) cc_final: 0.7497 (m) REVERT: B 714 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8378 (mtt) REVERT: C 9 ASP cc_start: 0.8778 (m-30) cc_final: 0.8515 (m-30) REVERT: C 195 ASP cc_start: 0.8112 (p0) cc_final: 0.7874 (p0) outliers start: 15 outliers final: 10 residues processed: 132 average time/residue: 2.3082 time to fit residues: 341.8902 Evaluate side-chains 135 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 146 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14518 Z= 0.299 Angle : 0.589 26.522 19687 Z= 0.302 Chirality : 0.039 0.246 2162 Planarity : 0.004 0.039 2456 Dihedral : 9.928 73.552 2207 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.99 % Allowed : 12.05 % Favored : 86.96 % 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: -0.11 (0.20), residues: 1692 helix: 1.29 (0.19), residues: 796 sheet: -0.79 (0.39), residues: 165 loop : -1.46 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.003 0.001 HIS B 562 PHE 0.088 0.002 PHE A 4 TYR 0.010 0.001 TYR A 110 ARG 0.003 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8579 (t80) cc_final: 0.8248 (t80) REVERT: A 88 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: B 714 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8389 (mtt) REVERT: C 9 ASP cc_start: 0.8796 (m-30) cc_final: 0.8539 (m-30) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 2.1555 time to fit residues: 311.2801 Evaluate side-chains 130 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 195 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14518 Z= 0.326 Angle : 0.593 25.623 19687 Z= 0.302 Chirality : 0.039 0.143 2162 Planarity : 0.004 0.035 2456 Dihedral : 9.932 73.568 2207 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.93 % Allowed : 12.11 % Favored : 86.96 % 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: -0.13 (0.20), residues: 1692 helix: 1.28 (0.19), residues: 797 sheet: -0.77 (0.40), residues: 165 loop : -1.48 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 406 HIS 0.003 0.001 HIS B 562 PHE 0.048 0.002 PHE A 446 TYR 0.013 0.001 TYR A 110 ARG 0.003 0.000 ARG A 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8578 (t80) cc_final: 0.8242 (t80) REVERT: A 88 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7626 (m-10) REVERT: B 649 HIS cc_start: 0.6929 (m-70) cc_final: 0.6700 (m170) REVERT: B 714 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: C 9 ASP cc_start: 0.8790 (m-30) cc_final: 0.8532 (m-30) REVERT: C 195 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7806 (p0) outliers start: 14 outliers final: 9 residues processed: 129 average time/residue: 2.4103 time to fit residues: 348.8210 Evaluate side-chains 133 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 195 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069093 restraints weight = 90344.662| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.74 r_work: 0.3022 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14518 Z= 0.171 Angle : 0.561 26.868 19687 Z= 0.278 Chirality : 0.037 0.146 2162 Planarity : 0.003 0.035 2456 Dihedral : 9.810 73.418 2207 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.86 % Allowed : 12.31 % Favored : 86.83 % 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: 0.07 (0.21), residues: 1692 helix: 1.43 (0.19), residues: 798 sheet: -0.72 (0.39), residues: 170 loop : -1.36 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.003 0.001 HIS A 41 PHE 0.027 0.001 PHE A 4 TYR 0.012 0.001 TYR A 110 ARG 0.002 0.000 ARG C 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8285.47 seconds wall clock time: 147 minutes 18.48 seconds (8838.48 seconds total)