Starting phenix.real_space_refine on Wed Mar 20 22:20:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk2_12429/03_2024/7nk2_12429.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk2_12429/03_2024/7nk2_12429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk2_12429/03_2024/7nk2_12429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk2_12429/03_2024/7nk2_12429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk2_12429/03_2024/7nk2_12429.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nk2_12429/03_2024/7nk2_12429.pdb" } resolution = 4.84 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= 0.027 sd= 0.342 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 107 5.16 5 C 9311 2.51 5 N 2595 2.21 5 O 2872 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 28776 Number of models: 1 Model: "" Number of chains: 6 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} Chain: "F" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 727 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 3 Time building chain proxies: 12.72, per 1000 atoms: 0.44 Number of scatterers: 28776 At special positions: 0 Unit cell: (102, 134, 138, 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 107 16.00 P 23 15.00 O 2872 8.00 N 2595 7.00 C 9311 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.01 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: 24.80 Conformation dependent library (CDL) restraints added in 3.2 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.6% alpha, 14.5% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 12.95 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: 5.021A 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: 3.792A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.432A 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: 3.637A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.629A 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: 4.634A 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: 3.973A 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: 3.778A 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: 3.509A 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: 3.595A 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: 4.035A 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: 4.236A 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: 4.300A 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 helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A 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: 3.837A 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: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A 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: 5.686A 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: 4.610A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.515A 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: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A 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: 8.344A 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: 3.518A 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: 3.882A 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 Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.158A pdb=" N GLY F 10 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.158A pdb=" N GLY F 10 " --> pdb=" O THR F 121 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1986 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: 10.51 Time building geometry restraints manager: 25.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13841 1.04 - 1.23: 792 1.23 - 1.43: 5751 1.43 - 1.63: 8555 1.63 - 1.83: 185 Bond restraints: 29124 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.523 -0.065 1.40e-02 5.10e+03 2.16e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 1.515 1.486 0.029 9.30e-03 1.16e+04 9.64e+00 bond pdb=" CD ARG F 38 " pdb=" NE ARG F 38 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.40e-02 5.10e+03 8.55e+00 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.40e-02 5.10e+03 7.87e+00 ... (remaining 29119 not shown) Histogram of bond angle deviations from ideal: 79.77 - 91.57: 6 91.57 - 103.37: 202 103.37 - 115.17: 36390 115.17 - 126.97: 15430 126.97 - 138.77: 241 Bond angle restraints: 52269 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 79.77 28.23 3.00e+00 1.11e-01 8.86e+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 80.32 27.68 3.00e+00 1.11e-01 8.52e+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 81.91 27.09 3.00e+00 1.11e-01 8.15e+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 82.47 26.53 3.00e+00 1.11e-01 7.82e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.77 -26.87 3.20e+00 9.77e-02 7.05e+01 ... (remaining 52264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12557 17.92 - 35.84: 867 35.84 - 53.76: 251 53.76 - 71.68: 90 71.68 - 89.60: 17 Dihedral angle restraints: 13782 sinusoidal: 7733 harmonic: 6049 Sorted by residual: dihedral pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual 122.80 138.40 -15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C SER F 85 " pdb=" N SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 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 ... (remaining 13779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2200 0.112 - 0.224: 60 0.224 - 0.336: 3 0.336 - 0.448: 2 0.448 - 0.560: 1 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CA SER F 85 " pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CB SER F 85 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA LYS F 65 " pdb=" N LYS F 65 " pdb=" C LYS F 65 " pdb=" CB LYS F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA ASN F 77 " pdb=" N ASN F 77 " pdb=" C ASN F 77 " pdb=" CB ASN F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 2263 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 59 " 0.057 2.00e-02 2.50e+03 4.05e-02 3.28e+01 pdb=" CG TYR F 59 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR F 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR F 59 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F 59 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 59 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR F 59 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 59 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 114 " -0.070 2.00e-02 2.50e+03 3.31e-02 2.74e+01 pdb=" CG TRP F 114 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP F 114 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP F 114 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP F 114 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 114 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 114 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 114 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 114 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP F 114 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 72 " -0.212 9.50e-02 1.11e+02 9.82e-02 1.28e+01 pdb=" NE ARG F 72 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG F 72 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG F 72 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 72 " -0.022 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1262 2.17 - 2.78: 56222 2.78 - 3.39: 80820 3.39 - 3.99: 105815 3.99 - 4.60: 165098 Nonbonded interactions: 409217 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.567 1.850 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 1.850 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.595 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 1.620 1.850 ... (remaining 409212 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 group one per residue 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: 0.160 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: 0.500 Extract box with map and model: 2.490 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 102.220 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4462 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 : 0.004 0.065 15256 Z= 0.273 Angle : 0.730 26.871 20676 Z= 0.429 Chirality : 0.046 0.560 2266 Planarity : 0.005 0.098 2583 Dihedral : 14.374 89.602 5967 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.32 % Allowed : 0.38 % Favored : 99.31 % Cbeta Deviations : 0.12 % 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 (0.19), residues: 1778 helix: 0.45 (0.19), residues: 786 sheet: -0.63 (0.37), residues: 180 loop : -1.32 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP F 114 HIS 0.003 0.001 HIS A 41 PHE 0.048 0.002 PHE A 446 TYR 0.073 0.002 TYR F 59 ARG 0.047 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 468 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 463 time to evaluate : 2.370 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: 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: 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: 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: 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 182 MET cc_start: -0.8027 (mpp) cc_final: -0.8853 (mtt) REVERT: A 268 LEU cc_start: 0.7539 (mt) cc_final: 0.7313 (mp) REVERT: A 437 HIS cc_start: 0.7692 (m90) cc_final: 0.5796 (m90) REVERT: A 453 CYS cc_start: 0.9115 (t) cc_final: 0.8901 (t) REVERT: A 489 CYS cc_start: 0.8462 (p) cc_final: 0.8250 (p) REVERT: A 644 SER cc_start: 0.8863 (m) cc_final: 0.8221 (t) REVERT: B 22 PHE cc_start: 0.6950 (m-80) cc_final: 0.5808 (m-80) REVERT: B 25 THR cc_start: 0.9254 (p) cc_final: 0.8981 (p) REVERT: B 28 PRO cc_start: 0.6716 (Cg_endo) cc_final: 0.6135 (Cg_exo) REVERT: B 43 VAL cc_start: 0.8472 (t) cc_final: 0.8255 (t) REVERT: B 92 MET cc_start: 0.7829 (mmm) cc_final: 0.7352 (mmm) REVERT: B 314 ASN cc_start: 0.8203 (t0) cc_final: 0.7653 (t0) REVERT: B 414 MET cc_start: 0.7615 (mmm) cc_final: 0.6976 (mmm) REVERT: B 485 ASN cc_start: 0.5524 (p0) cc_final: 0.4650 (p0) REVERT: B 493 THR cc_start: 0.8654 (m) cc_final: 0.8429 (p) REVERT: B 525 ILE cc_start: 0.9340 (mt) cc_final: 0.8988 (tp) REVERT: B 568 ILE cc_start: 0.8010 (mt) cc_final: 0.7792 (mt) REVERT: B 645 MET cc_start: 0.4828 (mpp) cc_final: 0.4489 (mtp) REVERT: B 721 ARG cc_start: 0.5446 (ttt-90) cc_final: 0.3430 (tpt170) REVERT: C 232 LEU cc_start: 0.5063 (tp) cc_final: 0.4732 (tp) REVERT: F 68 PHE cc_start: 0.7775 (m-10) cc_final: 0.6119 (m-10) outliers start: 5 outliers final: 1 residues processed: 467 average time/residue: 0.6535 time to fit residues: 432.5160 Evaluate side-chains 297 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 139 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 306 ASN B 312 ASN B 425 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4849 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 15256 Z= 0.197 Angle : 0.559 27.286 20676 Z= 0.297 Chirality : 0.038 0.144 2266 Planarity : 0.004 0.066 2583 Dihedral : 10.087 73.286 2307 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.85 % 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: -0.52 (0.19), residues: 1778 helix: 0.56 (0.19), residues: 795 sheet: -0.63 (0.35), residues: 196 loop : -1.16 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS B 605 PHE 0.018 0.002 PHE A 446 TYR 0.011 0.001 TYR A 540 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 334 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 2.219 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: 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: 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: 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: 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: 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 182 MET cc_start: -0.7736 (mpp) cc_final: -0.8766 (mtt) REVERT: A 268 LEU cc_start: 0.8316 (mt) cc_final: 0.8103 (mp) REVERT: A 410 GLU cc_start: 0.6836 (tt0) cc_final: 0.6024 (tt0) REVERT: A 682 ASP cc_start: 0.7616 (t0) cc_final: 0.6759 (t0) REVERT: B 18 ILE cc_start: 0.7215 (tp) cc_final: 0.6592 (tp) REVERT: B 22 PHE cc_start: 0.7419 (m-80) cc_final: 0.6765 (m-80) REVERT: B 25 THR cc_start: 0.9263 (p) cc_final: 0.8916 (p) REVERT: B 40 MET cc_start: 0.8621 (mtm) cc_final: 0.8106 (ptp) REVERT: B 179 MET cc_start: 0.7687 (mtp) cc_final: 0.7163 (ttm) REVERT: B 289 MET cc_start: 0.6836 (mmp) cc_final: 0.6500 (mmt) REVERT: B 321 MET cc_start: 0.6181 (mtp) cc_final: 0.5849 (mtp) REVERT: B 343 MET cc_start: 0.7026 (mtp) cc_final: 0.6398 (mtp) REVERT: B 348 MET cc_start: 0.6860 (mmm) cc_final: 0.5861 (mmt) REVERT: B 373 LEU cc_start: 0.8554 (mt) cc_final: 0.8198 (mt) REVERT: B 414 MET cc_start: 0.7454 (mmm) cc_final: 0.6503 (mmm) REVERT: B 442 GLN cc_start: 0.7886 (tp40) cc_final: 0.7614 (mm-40) REVERT: B 525 ILE cc_start: 0.9353 (mt) cc_final: 0.8867 (tp) REVERT: C 4 ILE cc_start: 0.4570 (tt) cc_final: 0.3857 (mm) REVERT: C 11 MET cc_start: 0.6655 (mmt) cc_final: 0.6416 (mmt) REVERT: C 166 VAL cc_start: 0.3943 (t) cc_final: 0.2784 (p) REVERT: C 232 LEU cc_start: 0.4213 (tp) cc_final: 0.3983 (tp) REVERT: F 34 MET cc_start: 0.5520 (mmp) cc_final: 0.5138 (mmm) REVERT: F 68 PHE cc_start: 0.7961 (m-10) cc_final: 0.6446 (m-10) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.6231 time to fit residues: 300.7585 Evaluate side-chains 267 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 312 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 15256 Z= 0.406 Angle : 0.776 25.893 20676 Z= 0.424 Chirality : 0.042 0.196 2266 Planarity : 0.007 0.188 2583 Dihedral : 10.431 73.357 2307 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 1778 helix: -0.32 (0.17), residues: 807 sheet: -0.69 (0.36), residues: 198 loop : -1.63 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 36 HIS 0.018 0.002 HIS A 326 PHE 0.038 0.003 PHE F 47 TYR 0.017 0.002 TYR B 82 ARG 0.014 0.001 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 305 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 303 time to evaluate : 2.390 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.0734 (mpp) cc_final: 0.0276 (mtt) REVERT: A 155 MET cc_start: -0.4941 (ptm) cc_final: -0.5478 (ptm) REVERT: A 182 MET cc_start: -0.7592 (mpp) cc_final: -0.8784 (mtt) REVERT: A 249 MET cc_start: 0.8101 (ttm) cc_final: 0.7756 (ttm) REVERT: A 253 VAL cc_start: 0.9296 (t) cc_final: 0.8998 (t) REVERT: A 370 LEU cc_start: 0.8497 (mt) cc_final: 0.8218 (mt) REVERT: A 473 SER cc_start: 0.9604 (m) cc_final: 0.9272 (p) REVERT: A 682 ASP cc_start: 0.8864 (t0) cc_final: 0.8520 (t0) REVERT: A 697 ASP cc_start: 0.9023 (t0) cc_final: 0.7826 (m-30) REVERT: B 22 PHE cc_start: 0.7807 (m-80) cc_final: 0.7381 (m-80) REVERT: B 25 THR cc_start: 0.9154 (p) cc_final: 0.8714 (p) REVERT: B 246 MET cc_start: 0.7908 (pmm) cc_final: 0.7423 (pmm) REVERT: B 452 ASN cc_start: 0.7837 (m-40) cc_final: 0.7490 (t0) REVERT: B 525 ILE cc_start: 0.9440 (mt) cc_final: 0.8904 (tp) REVERT: B 673 SER cc_start: 0.8571 (t) cc_final: 0.8137 (p) REVERT: C 4 ILE cc_start: 0.5462 (tt) cc_final: 0.4664 (mm) REVERT: C 23 THR cc_start: 0.7720 (m) cc_final: 0.7160 (m) REVERT: C 137 ASN cc_start: 0.4606 (t0) cc_final: 0.4340 (t0) REVERT: C 232 LEU cc_start: 0.4692 (tp) cc_final: 0.4356 (tp) REVERT: F 83 MET cc_start: 0.7663 (mtp) cc_final: 0.6979 (mtm) REVERT: F 90 ASP cc_start: 0.8298 (m-30) cc_final: 0.8001 (m-30) REVERT: F 120 VAL cc_start: 0.8223 (t) cc_final: 0.7931 (t) outliers start: 2 outliers final: 1 residues processed: 305 average time/residue: 0.6238 time to fit residues: 274.4220 Evaluate side-chains 251 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN B 47 HIS B 425 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15256 Z= 0.226 Angle : 0.605 29.010 20676 Z= 0.320 Chirality : 0.038 0.160 2266 Planarity : 0.005 0.067 2583 Dihedral : 10.341 78.566 2307 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -0.95 (0.19), residues: 1778 helix: 0.29 (0.18), residues: 800 sheet: -0.66 (0.37), residues: 199 loop : -1.56 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 36 HIS 0.012 0.002 HIS A 144 PHE 0.022 0.002 PHE F 47 TYR 0.013 0.002 TYR B 559 ARG 0.009 0.001 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 302 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.246 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: 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: 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: 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: 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 182 MET cc_start: -0.7364 (mpp) cc_final: -0.8687 (mtt) REVERT: A 249 MET cc_start: 0.7992 (ttm) cc_final: 0.7782 (ttm) REVERT: A 253 VAL cc_start: 0.9101 (t) cc_final: 0.8825 (t) REVERT: A 370 LEU cc_start: 0.8563 (mt) cc_final: 0.8346 (mt) REVERT: A 410 GLU cc_start: 0.7459 (tt0) cc_final: 0.7251 (tt0) REVERT: A 473 SER cc_start: 0.9544 (m) cc_final: 0.9250 (p) REVERT: A 548 MET cc_start: 0.8689 (ttt) cc_final: 0.8488 (ttp) REVERT: A 647 ASN cc_start: 0.9203 (m-40) cc_final: 0.8865 (m-40) REVERT: A 682 ASP cc_start: 0.8984 (t0) cc_final: 0.8647 (t0) REVERT: A 697 ASP cc_start: 0.9086 (t0) cc_final: 0.8378 (m-30) REVERT: B 19 SER cc_start: 0.8505 (p) cc_final: 0.8238 (p) REVERT: B 43 VAL cc_start: 0.8857 (t) cc_final: 0.8573 (t) REVERT: B 246 MET cc_start: 0.7690 (pmm) cc_final: 0.7210 (pmm) REVERT: B 314 ASN cc_start: 0.8313 (t0) cc_final: 0.7973 (t0) REVERT: B 411 MET cc_start: 0.8277 (mpp) cc_final: 0.7831 (mmt) REVERT: B 525 ILE cc_start: 0.9489 (mt) cc_final: 0.9063 (tp) REVERT: B 673 SER cc_start: 0.8369 (t) cc_final: 0.7938 (p) REVERT: F 83 MET cc_start: 0.7314 (mtp) cc_final: 0.6963 (mtm) REVERT: F 90 ASP cc_start: 0.8176 (m-30) cc_final: 0.7912 (m-30) REVERT: F 120 VAL cc_start: 0.8397 (t) cc_final: 0.8003 (t) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.6189 time to fit residues: 278.3651 Evaluate side-chains 252 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN C 75 GLN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 15256 Z= 0.366 Angle : 0.759 27.575 20676 Z= 0.411 Chirality : 0.041 0.155 2266 Planarity : 0.006 0.065 2583 Dihedral : 10.713 89.941 2307 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 1778 helix: -0.30 (0.17), residues: 808 sheet: -0.92 (0.37), residues: 190 loop : -2.07 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 338 HIS 0.010 0.002 HIS B 664 PHE 0.019 0.002 PHE B 730 TYR 0.038 0.003 TYR B 30 ARG 0.014 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 281 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.410 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: 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: 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: 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: 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 155 MET cc_start: -0.4614 (ptm) cc_final: -0.5337 (ptm) REVERT: A 182 MET cc_start: -0.7131 (mpp) cc_final: -0.8572 (mtt) REVERT: A 211 MET cc_start: 0.6585 (mmm) cc_final: 0.6178 (mmm) REVERT: A 230 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7117 (ptp-110) REVERT: A 577 TRP cc_start: 0.8565 (m100) cc_final: 0.8269 (m100) REVERT: A 647 ASN cc_start: 0.9388 (m-40) cc_final: 0.9079 (m-40) REVERT: A 697 ASP cc_start: 0.9182 (t0) cc_final: 0.8285 (m-30) REVERT: B 22 PHE cc_start: 0.7760 (m-80) cc_final: 0.7450 (m-80) REVERT: B 25 THR cc_start: 0.8921 (p) cc_final: 0.8437 (p) REVERT: B 77 ASN cc_start: 0.8614 (m-40) cc_final: 0.8228 (p0) REVERT: B 246 MET cc_start: 0.7757 (pmm) cc_final: 0.7348 (pmm) REVERT: B 267 GLU cc_start: 0.7515 (tt0) cc_final: 0.6820 (tm-30) REVERT: B 452 ASN cc_start: 0.7990 (m-40) cc_final: 0.7465 (t0) REVERT: B 459 ILE cc_start: 0.8965 (mm) cc_final: 0.8699 (mm) REVERT: B 646 MET cc_start: 0.1591 (mtm) cc_final: 0.1368 (mtp) REVERT: B 673 SER cc_start: 0.8294 (t) cc_final: 0.7833 (p) REVERT: C 90 MET cc_start: 0.2646 (tpp) cc_final: 0.2324 (tpp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.5844 time to fit residues: 243.1404 Evaluate side-chains 240 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15256 Z= 0.226 Angle : 0.618 27.258 20676 Z= 0.329 Chirality : 0.039 0.176 2266 Planarity : 0.005 0.056 2583 Dihedral : 10.680 94.209 2307 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 1778 helix: 0.18 (0.18), residues: 807 sheet: -0.88 (0.37), residues: 193 loop : -1.98 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 577 HIS 0.005 0.001 HIS A 510 PHE 0.023 0.002 PHE F 47 TYR 0.015 0.002 TYR B 49 ARG 0.010 0.001 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 281 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.367 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: 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: 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: 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: 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 155 MET cc_start: -0.4615 (ptm) cc_final: -0.5350 (ptm) REVERT: A 182 MET cc_start: -0.7163 (mpp) cc_final: -0.8549 (mtt) REVERT: A 211 MET cc_start: 0.6539 (mmm) cc_final: 0.6335 (mmm) REVERT: A 516 ASP cc_start: 0.8672 (m-30) cc_final: 0.8204 (t70) REVERT: A 517 VAL cc_start: 0.8909 (t) cc_final: 0.8604 (m) REVERT: A 647 ASN cc_start: 0.9440 (m-40) cc_final: 0.9134 (m-40) REVERT: A 676 LEU cc_start: 0.8502 (mt) cc_final: 0.8302 (mt) REVERT: A 697 ASP cc_start: 0.9059 (t0) cc_final: 0.8257 (m-30) REVERT: B 22 PHE cc_start: 0.7658 (m-80) cc_final: 0.7366 (m-80) REVERT: B 25 THR cc_start: 0.8924 (p) cc_final: 0.8658 (p) REVERT: B 171 MET cc_start: 0.8938 (mtm) cc_final: 0.8692 (mtm) REVERT: B 246 MET cc_start: 0.7736 (pmm) cc_final: 0.7225 (pmm) REVERT: B 267 GLU cc_start: 0.7391 (tt0) cc_final: 0.6852 (tm-30) REVERT: B 331 GLU cc_start: 0.7096 (pm20) cc_final: 0.6349 (pp20) REVERT: B 362 MET cc_start: 0.7946 (mmm) cc_final: 0.7541 (mmp) REVERT: B 452 ASN cc_start: 0.8144 (m-40) cc_final: 0.7587 (t0) REVERT: B 459 ILE cc_start: 0.9070 (mm) cc_final: 0.8799 (mm) REVERT: B 525 ILE cc_start: 0.9474 (mt) cc_final: 0.9085 (tp) REVERT: B 546 MET cc_start: 0.8586 (mmt) cc_final: 0.8185 (mmm) REVERT: C 23 THR cc_start: 0.7869 (m) cc_final: 0.7565 (m) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.5956 time to fit residues: 251.1191 Evaluate side-chains 245 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.7625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15256 Z= 0.185 Angle : 0.578 27.484 20676 Z= 0.305 Chirality : 0.037 0.142 2266 Planarity : 0.005 0.123 2583 Dihedral : 10.558 95.955 2307 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1778 helix: 0.44 (0.18), residues: 806 sheet: -0.77 (0.38), residues: 186 loop : -1.89 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 666 HIS 0.007 0.001 HIS C 27 PHE 0.019 0.002 PHE A 176 TYR 0.015 0.001 TYR B 555 ARG 0.006 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 275 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.083 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: 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: 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: 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: 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 155 MET cc_start: -0.4568 (ptm) cc_final: -0.5309 (ptm) REVERT: A 182 MET cc_start: -0.7079 (mpp) cc_final: -0.8477 (mtt) REVERT: A 367 LYS cc_start: 0.6707 (mttp) cc_final: 0.6396 (mttt) REVERT: A 460 MET cc_start: 0.8938 (mmt) cc_final: 0.8690 (mmt) REVERT: A 516 ASP cc_start: 0.8589 (m-30) cc_final: 0.8213 (t70) REVERT: A 517 VAL cc_start: 0.8892 (t) cc_final: 0.8567 (m) REVERT: A 528 THR cc_start: 0.7564 (m) cc_final: 0.7047 (m) REVERT: A 647 ASN cc_start: 0.9291 (m-40) cc_final: 0.9004 (m-40) REVERT: A 676 LEU cc_start: 0.8690 (mt) cc_final: 0.8381 (mt) REVERT: A 697 ASP cc_start: 0.9052 (t0) cc_final: 0.8260 (m-30) REVERT: B 22 PHE cc_start: 0.7685 (m-80) cc_final: 0.7421 (m-80) REVERT: B 25 THR cc_start: 0.8941 (p) cc_final: 0.8548 (p) REVERT: B 44 ASN cc_start: 0.8976 (m-40) cc_final: 0.8637 (m-40) REVERT: B 92 MET cc_start: 0.8762 (mmm) cc_final: 0.7847 (mmm) REVERT: B 246 MET cc_start: 0.7463 (pmm) cc_final: 0.7131 (pmm) REVERT: B 267 GLU cc_start: 0.7341 (tt0) cc_final: 0.6756 (tm-30) REVERT: B 331 GLU cc_start: 0.7114 (pm20) cc_final: 0.6445 (pp20) REVERT: B 525 ILE cc_start: 0.9478 (mt) cc_final: 0.9068 (tp) REVERT: B 546 MET cc_start: 0.9078 (mmt) cc_final: 0.8583 (mmm) REVERT: C 11 MET cc_start: 0.7397 (mmt) cc_final: 0.6980 (mmm) REVERT: C 23 THR cc_start: 0.7834 (m) cc_final: 0.7570 (m) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.5560 time to fit residues: 228.4845 Evaluate side-chains 245 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 425 ASN F 3 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.8441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15256 Z= 0.288 Angle : 0.665 27.407 20676 Z= 0.356 Chirality : 0.039 0.154 2266 Planarity : 0.005 0.063 2583 Dihedral : 10.772 100.781 2307 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 1778 helix: 0.10 (0.18), residues: 805 sheet: -0.99 (0.38), residues: 179 loop : -2.01 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 577 HIS 0.005 0.001 HIS B 664 PHE 0.016 0.002 PHE A 611 TYR 0.018 0.002 TYR A 687 ARG 0.007 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 263 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.428 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: -0.4307 (ptm) cc_final: -0.5152 (ptm) REVERT: A 182 MET cc_start: -0.7342 (mpp) cc_final: -0.8716 (mtt) REVERT: A 516 ASP cc_start: 0.8887 (m-30) cc_final: 0.8669 (t70) REVERT: A 577 TRP cc_start: 0.8100 (m100) cc_final: 0.7534 (m-10) REVERT: A 647 ASN cc_start: 0.9384 (m-40) cc_final: 0.9101 (m-40) REVERT: A 676 LEU cc_start: 0.8776 (mt) cc_final: 0.8405 (mp) REVERT: A 682 ASP cc_start: 0.8587 (t0) cc_final: 0.7540 (p0) REVERT: A 697 ASP cc_start: 0.9093 (t0) cc_final: 0.8313 (m-30) REVERT: B 25 THR cc_start: 0.8805 (p) cc_final: 0.8522 (p) REVERT: B 246 MET cc_start: 0.7621 (pmm) cc_final: 0.7229 (pmm) REVERT: B 267 GLU cc_start: 0.7557 (tt0) cc_final: 0.6942 (tm-30) REVERT: B 331 GLU cc_start: 0.6818 (pm20) cc_final: 0.6204 (pp20) REVERT: B 348 MET cc_start: 0.6853 (mmm) cc_final: 0.6216 (mmm) REVERT: B 452 ASN cc_start: 0.8022 (m-40) cc_final: 0.7722 (t0) REVERT: B 525 ILE cc_start: 0.9499 (mt) cc_final: 0.9086 (tp) REVERT: C 11 MET cc_start: 0.7413 (mmt) cc_final: 0.7015 (mmm) REVERT: C 90 MET cc_start: 0.3426 (tpp) cc_final: 0.3059 (tpp) REVERT: F 120 VAL cc_start: 0.8761 (t) cc_final: 0.8438 (t) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.5535 time to fit residues: 218.7147 Evaluate side-chains 227 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN B 425 ASN ** B 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.8780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15256 Z= 0.240 Angle : 0.625 27.353 20676 Z= 0.332 Chirality : 0.038 0.177 2266 Planarity : 0.005 0.079 2583 Dihedral : 10.763 101.823 2307 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1778 helix: 0.22 (0.18), residues: 803 sheet: -1.00 (0.37), residues: 172 loop : -2.00 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 577 HIS 0.009 0.001 HIS A 510 PHE 0.017 0.002 PHE F 47 TYR 0.019 0.002 TYR B 355 ARG 0.008 0.001 ARG A 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 265 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.047 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: -0.4090 (ptm) cc_final: -0.5035 (ptm) REVERT: A 182 MET cc_start: -0.7216 (mpp) cc_final: -0.8610 (mtt) REVERT: A 460 MET cc_start: 0.9138 (mmt) cc_final: 0.8857 (mmt) REVERT: A 603 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8207 (mmtt) REVERT: A 647 ASN cc_start: 0.9264 (m-40) cc_final: 0.9056 (m-40) REVERT: A 676 LEU cc_start: 0.8792 (mt) cc_final: 0.8415 (mp) REVERT: A 682 ASP cc_start: 0.8554 (t0) cc_final: 0.7468 (p0) REVERT: A 697 ASP cc_start: 0.9062 (t0) cc_final: 0.8355 (m-30) REVERT: B 92 MET cc_start: 0.8854 (mmm) cc_final: 0.8003 (mmm) REVERT: B 246 MET cc_start: 0.7609 (pmm) cc_final: 0.7174 (pmm) REVERT: B 256 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 267 GLU cc_start: 0.7501 (tt0) cc_final: 0.6953 (tm-30) REVERT: B 314 ASN cc_start: 0.8455 (t0) cc_final: 0.8150 (t0) REVERT: B 331 GLU cc_start: 0.6695 (pm20) cc_final: 0.6392 (pp20) REVERT: B 452 ASN cc_start: 0.8111 (m-40) cc_final: 0.7700 (t0) REVERT: B 525 ILE cc_start: 0.9471 (mt) cc_final: 0.9068 (tp) REVERT: B 604 LEU cc_start: 0.8659 (tp) cc_final: 0.8379 (tp) REVERT: C 90 MET cc_start: 0.3480 (tpp) cc_final: 0.3174 (tpp) REVERT: F 81 LEU cc_start: 0.7471 (tt) cc_final: 0.7054 (tt) REVERT: F 120 VAL cc_start: 0.8686 (t) cc_final: 0.8455 (t) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.5450 time to fit residues: 217.1211 Evaluate side-chains 226 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 chunk 163 optimal weight: 0.0470 chunk 141 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 109 optimal weight: 0.4980 chunk 86 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 425 ASN ** B 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.8859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15256 Z= 0.166 Angle : 0.576 26.988 20676 Z= 0.298 Chirality : 0.038 0.183 2266 Planarity : 0.004 0.061 2583 Dihedral : 10.592 101.055 2307 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: -0.83 (0.19), residues: 1778 helix: 0.65 (0.18), residues: 808 sheet: -0.81 (0.39), residues: 167 loop : -1.77 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 36 HIS 0.012 0.001 HIS A 510 PHE 0.017 0.001 PHE B 496 TYR 0.012 0.001 TYR B 555 ARG 0.007 0.000 ARG A 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 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 266 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.461 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: -0.4166 (ptm) cc_final: -0.5090 (ptm) REVERT: A 182 MET cc_start: -0.7156 (mpp) cc_final: -0.8566 (mtt) REVERT: A 460 MET cc_start: 0.9094 (mmt) cc_final: 0.8846 (mmt) REVERT: A 523 MET cc_start: 0.6057 (mtp) cc_final: 0.5246 (mtp) REVERT: A 573 ILE cc_start: 0.9220 (pt) cc_final: 0.8763 (tt) REVERT: A 603 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8126 (mmtt) REVERT: A 676 LEU cc_start: 0.8782 (mt) cc_final: 0.8426 (mp) REVERT: A 682 ASP cc_start: 0.8544 (t0) cc_final: 0.7394 (p0) REVERT: A 697 ASP cc_start: 0.9057 (t0) cc_final: 0.8239 (m-30) REVERT: B 65 GLN cc_start: 0.8526 (mp10) cc_final: 0.8229 (mp10) REVERT: B 92 MET cc_start: 0.8800 (mmm) cc_final: 0.7794 (mmm) REVERT: B 246 MET cc_start: 0.7321 (pmm) cc_final: 0.7085 (pmm) REVERT: B 256 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7979 (mm-30) REVERT: B 331 GLU cc_start: 0.7458 (pm20) cc_final: 0.7188 (pp20) REVERT: B 507 MET cc_start: 0.2986 (mtm) cc_final: 0.2770 (tmm) REVERT: B 525 ILE cc_start: 0.9445 (mt) cc_final: 0.9045 (tp) REVERT: F 120 VAL cc_start: 0.8530 (t) cc_final: 0.8272 (t) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.5483 time to fit residues: 221.3058 Evaluate side-chains 231 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.166461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124776 restraints weight = 118653.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128904 restraints weight = 62748.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131952 restraints weight = 40913.964| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.9208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15256 Z= 0.251 Angle : 0.611 27.005 20676 Z= 0.328 Chirality : 0.039 0.241 2266 Planarity : 0.005 0.064 2583 Dihedral : 10.643 101.634 2307 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1778 helix: 0.45 (0.18), residues: 821 sheet: -0.93 (0.39), residues: 177 loop : -1.84 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 577 HIS 0.006 0.001 HIS A 510 PHE 0.039 0.002 PHE B 501 TYR 0.015 0.002 TYR A 687 ARG 0.009 0.001 ARG A 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6535.97 seconds wall clock time: 116 minutes 8.95 seconds (6968.95 seconds total)