Starting phenix.real_space_refine on Wed Mar 20 22:07:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/03_2024/7nki_12440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/03_2024/7nki_12440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/03_2024/7nki_12440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/03_2024/7nki_12440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/03_2024/7nki_12440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/03_2024/7nki_12440.pdb" } resolution = 4.67 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= 0.014 sd= 0.191 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 9310 2.51 5 N 2593 2.21 5 O 2874 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: 28775 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: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 3 Time building chain proxies: 12.49, per 1000 atoms: 0.43 Number of scatterers: 28775 At special positions: 0 Unit cell: (98, 106, 180, 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 2874 8.00 N 2593 7.00 C 9310 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 99 " distance=2.00 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: 23.24 Conformation dependent library (CDL) restraints added in 3.3 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: 3382 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.6% alpha, 14.7% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 13.96 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: 4.005A 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: 3.692A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A 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: 3.947A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.629A 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: 4.633A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.777A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.530A 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: 5.827A 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: 3.587A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.511A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.617A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.037A 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: 4.330A 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: 4.108A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.521A 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: 3.584A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.618A 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 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.022A 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: 4.714A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A 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: 11.080A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.516A 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: 6.633A 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: 4.809A 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: 6.557A 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: 6.514A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU 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: 6.514A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 11.67 Time building geometry restraints manager: 23.99 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 - 1.24: 1022 1.24 - 1.43: 5554 1.43 - 1.63: 8520 1.63 - 1.83: 185 Bond restraints: 29122 Sorted by residual: bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.40e-02 5.10e+03 6.99e+00 bond pdb=" CD ARG F 70 " pdb=" NE ARG F 70 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.40e-02 5.10e+03 6.41e+00 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.40e-02 5.10e+03 6.23e+00 bond pdb=" CA ASP F 76 " pdb=" CB ASP F 76 " ideal model delta sigma weight residual 1.528 1.562 -0.035 1.39e-02 5.18e+03 6.22e+00 bond pdb=" N GLN F 1 " pdb=" CA GLN F 1 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.90e-02 2.77e+03 6.08e+00 ... (remaining 29117 not shown) Histogram of bond angle deviations from ideal: 79.81 - 91.61: 4 91.61 - 103.42: 214 103.42 - 115.22: 36438 115.22 - 127.02: 15385 127.02 - 138.82: 230 Bond angle restraints: 52271 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 79.81 28.19 3.00e+00 1.11e-01 8.83e+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 8.51e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.92 27.08 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 111.90 138.82 -26.92 3.20e+00 9.77e-02 7.08e+01 ... (remaining 52266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12578 17.94 - 35.89: 850 35.89 - 53.83: 258 53.83 - 71.77: 83 71.77 - 89.72: 17 Dihedral angle restraints: 13786 sinusoidal: 7733 harmonic: 6053 Sorted by residual: dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP B 729 " pdb=" C ASP B 729 " pdb=" N PHE B 730 " pdb=" CA PHE B 730 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 13783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1887 0.049 - 0.099: 289 0.099 - 0.148: 79 0.148 - 0.198: 15 0.198 - 0.247: 2 Chirality restraints: 2272 Sorted by residual: chirality pdb=" CA THR F 81 " pdb=" N THR F 81 " pdb=" C THR F 81 " pdb=" CB THR F 81 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ASN F 80 " pdb=" N ASN F 80 " pdb=" C ASN F 80 " pdb=" CB ASN F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA THR F 119 " pdb=" N THR F 119 " pdb=" C THR F 119 " pdb=" CB THR F 119 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 2269 not shown) Planarity restraints: 4223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 100 " -0.088 2.00e-02 2.50e+03 7.63e-02 1.16e+02 pdb=" CG TYR F 100 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR F 100 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 100 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 100 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR F 100 " 0.078 2.00e-02 2.50e+03 pdb=" CZ TYR F 100 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR F 100 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 102 " 0.117 2.00e-02 2.50e+03 6.21e-02 7.71e+01 pdb=" CG TYR F 102 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR F 102 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR F 102 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR F 102 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 102 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR F 102 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 102 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.010 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" CG TYR F 37 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " 0.038 2.00e-02 2.50e+03 ... (remaining 4220 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1254 2.17 - 2.78: 56134 2.78 - 3.39: 80888 3.39 - 3.99: 105763 3.99 - 4.60: 165059 Nonbonded interactions: 409098 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.566 1.850 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 1.850 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 1.850 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 1.850 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 1.850 ... (remaining 409093 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.470 Extract box with map and model: 2.730 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 101.940 Find NCS groups from input model: 0.580 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4309 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 0.047 15254 Z= 0.254 Angle : 0.670 26.918 20678 Z= 0.391 Chirality : 0.042 0.247 2272 Planarity : 0.006 0.125 2582 Dihedral : 14.258 89.718 5969 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: -0.64 (0.20), residues: 1778 helix: 0.45 (0.19), residues: 786 sheet: -0.62 (0.38), residues: 177 loop : -1.21 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 36 HIS 0.003 0.001 HIS A 41 PHE 0.048 0.002 PHE A 446 TYR 0.152 0.004 TYR F 100 ARG 0.016 0.001 ARG F 70 *********************** 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 399 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 2.355 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: symmetry clash revert: symmetry clash revert: 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 211 MET cc_start: 0.3543 (tpt) cc_final: 0.3202 (tpp) REVERT: A 271 PRO cc_start: 0.6159 (Cg_endo) cc_final: 0.5575 (Cg_exo) REVERT: A 575 MET cc_start: 0.7816 (mtm) cc_final: 0.7489 (mtm) REVERT: A 581 MET cc_start: 0.7374 (mtp) cc_final: 0.6863 (mtp) REVERT: A 585 LEU cc_start: 0.8989 (mt) cc_final: 0.8690 (mm) REVERT: A 656 GLU cc_start: 0.6639 (mm-30) cc_final: 0.5775 (mm-30) REVERT: B 136 ASN cc_start: 0.8586 (m-40) cc_final: 0.8299 (m-40) REVERT: B 146 THR cc_start: 0.7925 (p) cc_final: 0.7703 (t) REVERT: B 344 PHE cc_start: 0.7674 (m-10) cc_final: 0.7243 (m-80) REVERT: B 413 ASN cc_start: 0.8254 (m110) cc_final: 0.7630 (p0) REVERT: B 528 THR cc_start: 0.7697 (m) cc_final: 0.6822 (p) REVERT: B 529 VAL cc_start: 0.9284 (t) cc_final: 0.8901 (p) REVERT: B 530 ILE cc_start: 0.8647 (mt) cc_final: 0.8342 (mt) REVERT: B 550 LEU cc_start: 0.7139 (mt) cc_final: 0.6765 (mt) REVERT: B 609 VAL cc_start: 0.4960 (t) cc_final: 0.4592 (t) REVERT: B 610 CYS cc_start: 0.7551 (m) cc_final: 0.6982 (t) REVERT: B 696 PHE cc_start: 0.7573 (t80) cc_final: 0.7219 (t80) REVERT: C 24 THR cc_start: 0.7797 (p) cc_final: 0.7493 (t) REVERT: F 88 MET cc_start: -0.1690 (mmm) cc_final: -0.3568 (mmp) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.7308 time to fit residues: 400.6322 Evaluate side-chains 267 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.242 ------------------------------------------------------------------------------- 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: 3.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 703 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN B 756 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4928 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15254 Z= 0.268 Angle : 0.630 27.522 20678 Z= 0.341 Chirality : 0.038 0.155 2272 Planarity : 0.005 0.048 2582 Dihedral : 10.182 73.528 2309 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.13 % Allowed : 2.39 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1778 helix: 0.27 (0.18), residues: 797 sheet: -0.94 (0.37), residues: 194 loop : -1.15 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 338 HIS 0.010 0.002 HIS B 32 PHE 0.021 0.002 PHE A 446 TYR 0.017 0.002 TYR B 620 ARG 0.004 0.001 ARG B 602 *********************** 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 300 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 2.510 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 ILE cc_start: 0.5409 (pt) cc_final: 0.4687 (tp) REVERT: A 464 TYR cc_start: 0.6755 (t80) cc_final: 0.6333 (t80) REVERT: A 575 MET cc_start: 0.8428 (mtm) cc_final: 0.7785 (mtm) REVERT: A 682 ASP cc_start: 0.7117 (t0) cc_final: 0.6908 (t0) REVERT: A 710 PHE cc_start: 0.7183 (p90) cc_final: 0.6731 (p90) REVERT: B 141 THR cc_start: 0.7803 (m) cc_final: 0.7562 (m) REVERT: B 146 THR cc_start: 0.8719 (p) cc_final: 0.8485 (t) REVERT: B 217 TYR cc_start: 0.6220 (t80) cc_final: 0.5972 (t80) REVERT: B 306 ASN cc_start: 0.6948 (m110) cc_final: 0.6534 (m110) REVERT: B 321 MET cc_start: 0.8218 (mtt) cc_final: 0.6779 (mtt) REVERT: B 343 MET cc_start: 0.8160 (mmm) cc_final: 0.7937 (mmm) REVERT: B 413 ASN cc_start: 0.8172 (m110) cc_final: 0.7351 (p0) REVERT: B 419 LEU cc_start: 0.8622 (tp) cc_final: 0.8413 (tt) REVERT: B 528 THR cc_start: 0.7547 (m) cc_final: 0.7291 (p) REVERT: B 529 VAL cc_start: 0.9171 (t) cc_final: 0.8904 (p) REVERT: B 530 ILE cc_start: 0.8707 (mt) cc_final: 0.8392 (mt) REVERT: B 610 CYS cc_start: 0.8186 (m) cc_final: 0.7480 (t) REVERT: C 1 MET cc_start: 0.4105 (mmm) cc_final: 0.3333 (mmm) REVERT: F 46 GLU cc_start: 0.3974 (pt0) cc_final: 0.2498 (tp30) REVERT: F 88 MET cc_start: -0.1028 (mmm) cc_final: -0.2759 (mmp) outliers start: 2 outliers final: 1 residues processed: 299 average time/residue: 0.7106 time to fit residues: 295.5383 Evaluate side-chains 249 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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: 0.9980 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 670 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 582 GLN C 27 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS F 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 15254 Z= 0.320 Angle : 0.684 25.556 20678 Z= 0.374 Chirality : 0.039 0.155 2272 Planarity : 0.006 0.081 2582 Dihedral : 10.197 73.487 2309 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.19 % Allowed : 2.83 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 1778 helix: 0.06 (0.17), residues: 812 sheet: -0.81 (0.38), residues: 182 loop : -1.61 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 99 HIS 0.011 0.002 HIS B 32 PHE 0.019 0.002 PHE B 730 TYR 0.021 0.002 TYR F 83 ARG 0.018 0.001 ARG B 238 *********************** 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 269 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 2.536 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 284 LEU cc_start: 0.7541 (mt) cc_final: 0.7073 (mp) REVERT: A 464 TYR cc_start: 0.6842 (t80) cc_final: 0.6465 (t80) REVERT: A 477 MET cc_start: 0.7354 (pmm) cc_final: 0.7072 (pmm) REVERT: A 575 MET cc_start: 0.7889 (mtm) cc_final: 0.7655 (mtm) REVERT: B 171 MET cc_start: 0.6184 (ptt) cc_final: 0.5894 (ptt) REVERT: B 219 ILE cc_start: 0.8064 (mt) cc_final: 0.7708 (mm) REVERT: B 238 ARG cc_start: 0.5684 (mmm160) cc_final: 0.5409 (mmm160) REVERT: B 306 ASN cc_start: 0.7234 (m110) cc_final: 0.7031 (m110) REVERT: B 313 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6526 (mm-40) REVERT: B 321 MET cc_start: 0.8320 (mtt) cc_final: 0.7046 (mtt) REVERT: B 528 THR cc_start: 0.7815 (m) cc_final: 0.7432 (p) REVERT: B 590 LEU cc_start: 0.8029 (mt) cc_final: 0.7824 (mm) REVERT: B 696 PHE cc_start: 0.7744 (t80) cc_final: 0.7519 (t80) REVERT: C 64 MET cc_start: 0.5934 (ttm) cc_final: 0.5663 (ttm) REVERT: F 34 MET cc_start: -0.0117 (mtt) cc_final: -0.0417 (mtt) REVERT: F 88 MET cc_start: -0.0995 (mmm) cc_final: -0.2398 (mmp) outliers start: 3 outliers final: 1 residues processed: 269 average time/residue: 0.6967 time to fit residues: 263.2027 Evaluate side-chains 219 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 217 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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: 0.9980 chunk 121 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 GLN B 313 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15254 Z= 0.184 Angle : 0.572 27.768 20678 Z= 0.302 Chirality : 0.038 0.154 2272 Planarity : 0.004 0.048 2582 Dihedral : 10.061 73.375 2309 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -0.62 (0.19), residues: 1778 helix: 0.53 (0.18), residues: 798 sheet: -0.60 (0.37), residues: 197 loop : -1.31 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 666 HIS 0.005 0.001 HIS B 32 PHE 0.018 0.001 PHE B 730 TYR 0.012 0.001 TYR B 657 ARG 0.016 0.001 ARG B 151 *********************** 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 252 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.345 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 284 LEU cc_start: 0.7351 (mt) cc_final: 0.6936 (mp) REVERT: A 464 TYR cc_start: 0.6625 (t80) cc_final: 0.6273 (t80) REVERT: A 575 MET cc_start: 0.7912 (mtm) cc_final: 0.7628 (mtm) REVERT: B 219 ILE cc_start: 0.8070 (mt) cc_final: 0.7686 (mm) REVERT: B 306 ASN cc_start: 0.7240 (m110) cc_final: 0.7014 (m110) REVERT: B 321 MET cc_start: 0.8382 (mtt) cc_final: 0.6891 (mtt) REVERT: B 528 THR cc_start: 0.7578 (m) cc_final: 0.7290 (p) REVERT: B 560 ARG cc_start: 0.7128 (mmt-90) cc_final: 0.6904 (mpt180) REVERT: C 45 LEU cc_start: 0.7337 (tt) cc_final: 0.7102 (tt) REVERT: C 64 MET cc_start: 0.6480 (ttm) cc_final: 0.6075 (ttm) REVERT: F 88 MET cc_start: -0.1151 (mmm) cc_final: -0.2740 (mmp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.7133 time to fit residues: 255.5003 Evaluate side-chains 214 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.253 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 0.0770 chunk 146 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15254 Z= 0.208 Angle : 0.573 27.034 20678 Z= 0.306 Chirality : 0.038 0.198 2272 Planarity : 0.004 0.065 2582 Dihedral : 10.082 73.529 2309 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: -0.57 (0.19), residues: 1778 helix: 0.68 (0.18), residues: 791 sheet: -0.63 (0.36), residues: 197 loop : -1.38 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 580 HIS 0.006 0.001 HIS B 32 PHE 0.018 0.002 PHE B 730 TYR 0.015 0.002 TYR F 83 ARG 0.006 0.001 ARG B 233 *********************** 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 234 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.983 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 464 TYR cc_start: 0.6786 (t80) cc_final: 0.6504 (t80) REVERT: A 575 MET cc_start: 0.7918 (mtm) cc_final: 0.7694 (mtm) REVERT: B 219 ILE cc_start: 0.8120 (mt) cc_final: 0.7634 (mm) REVERT: B 321 MET cc_start: 0.8436 (mtt) cc_final: 0.6912 (mtt) REVERT: B 348 MET cc_start: 0.5534 (mmt) cc_final: 0.5116 (mmt) REVERT: B 528 THR cc_start: 0.7579 (m) cc_final: 0.7190 (p) REVERT: B 696 PHE cc_start: 0.7814 (t80) cc_final: 0.7397 (t80) REVERT: C 50 MET cc_start: 0.7426 (ptt) cc_final: 0.6439 (ptt) REVERT: C 64 MET cc_start: 0.6920 (ttm) cc_final: 0.6610 (ttm) REVERT: F 88 MET cc_start: -0.1246 (mmm) cc_final: -0.2710 (mmp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.6629 time to fit residues: 220.8381 Evaluate side-chains 204 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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: 6.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 56 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5366 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15254 Z= 0.165 Angle : 0.541 26.991 20678 Z= 0.285 Chirality : 0.037 0.155 2272 Planarity : 0.004 0.049 2582 Dihedral : 10.000 75.608 2309 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -0.30 (0.20), residues: 1778 helix: 0.90 (0.18), residues: 792 sheet: -0.54 (0.36), residues: 200 loop : -1.24 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 368 HIS 0.007 0.001 HIS B 47 PHE 0.017 0.001 PHE B 730 TYR 0.012 0.001 TYR A 110 ARG 0.006 0.000 ARG B 162 *********************** 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 238 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.264 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: A 47 MET cc_start: 0.4513 (mtt) cc_final: 0.4098 (mtt) REVERT: A 464 TYR cc_start: 0.6726 (t80) cc_final: 0.6427 (t80) REVERT: A 581 MET cc_start: 0.7594 (mtm) cc_final: 0.7065 (mtm) REVERT: A 619 TRP cc_start: 0.6112 (m-90) cc_final: 0.5884 (m-90) REVERT: A 707 PHE cc_start: 0.7406 (t80) cc_final: 0.7153 (t80) REVERT: B 127 GLN cc_start: 0.7744 (mm110) cc_final: 0.6182 (mt0) REVERT: B 219 ILE cc_start: 0.8070 (mt) cc_final: 0.7588 (mm) REVERT: B 321 MET cc_start: 0.8365 (mtt) cc_final: 0.6859 (mtt) REVERT: B 348 MET cc_start: 0.5456 (mmt) cc_final: 0.5113 (mmt) REVERT: B 620 TYR cc_start: 0.7070 (t80) cc_final: 0.6537 (t80) REVERT: C 50 MET cc_start: 0.7368 (ptt) cc_final: 0.6493 (ptt) REVERT: C 64 MET cc_start: 0.6940 (ttm) cc_final: 0.6641 (ttm) REVERT: F 88 MET cc_start: -0.1292 (mmm) cc_final: -0.2815 (mmp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.6429 time to fit residues: 219.6715 Evaluate side-chains 207 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15254 Z= 0.204 Angle : 0.568 25.681 20678 Z= 0.306 Chirality : 0.038 0.251 2272 Planarity : 0.005 0.096 2582 Dihedral : 10.048 79.081 2309 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.39 (0.20), residues: 1778 helix: 0.79 (0.18), residues: 797 sheet: -0.53 (0.36), residues: 203 loop : -1.27 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 368 HIS 0.007 0.001 HIS B 32 PHE 0.019 0.002 PHE B 730 TYR 0.016 0.001 TYR F 83 ARG 0.007 0.001 ARG B 334 *********************** 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 240 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.269 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 464 TYR cc_start: 0.6734 (t80) cc_final: 0.6187 (t80) REVERT: A 581 MET cc_start: 0.7364 (mtm) cc_final: 0.7085 (mtm) REVERT: A 619 TRP cc_start: 0.5896 (m-90) cc_final: 0.5623 (m-90) REVERT: B 127 GLN cc_start: 0.7381 (mm-40) cc_final: 0.5871 (mt0) REVERT: B 348 MET cc_start: 0.5696 (mmt) cc_final: 0.5360 (mmt) REVERT: C 50 MET cc_start: 0.7401 (ptt) cc_final: 0.6486 (ptt) REVERT: C 202 MET cc_start: 0.7037 (mmm) cc_final: 0.6784 (mmm) REVERT: F 88 MET cc_start: -0.1848 (mmm) cc_final: -0.3241 (mmp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.6565 time to fit residues: 226.2556 Evaluate side-chains 211 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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: 6.9990 chunk 102 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 313 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15254 Z= 0.247 Angle : 0.625 28.389 20678 Z= 0.335 Chirality : 0.038 0.184 2272 Planarity : 0.005 0.057 2582 Dihedral : 10.243 83.684 2309 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1778 helix: 0.69 (0.18), residues: 789 sheet: -0.54 (0.38), residues: 194 loop : -1.38 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 368 HIS 0.009 0.001 HIS B 32 PHE 0.020 0.002 PHE A 710 TYR 0.033 0.002 TYR C 111 ARG 0.007 0.001 ARG A 583 *********************** 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 234 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.111 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 581 MET cc_start: 0.7664 (mtm) cc_final: 0.7278 (mtm) REVERT: A 619 TRP cc_start: 0.6167 (m-90) cc_final: 0.5909 (m-90) REVERT: B 126 ARG cc_start: 0.8951 (pmt-80) cc_final: 0.8444 (pmt-80) REVERT: B 127 GLN cc_start: 0.7719 (mm-40) cc_final: 0.6003 (mt0) REVERT: B 348 MET cc_start: 0.5827 (mmt) cc_final: 0.5511 (mmt) REVERT: B 403 LEU cc_start: 0.7764 (tp) cc_final: 0.7513 (tp) REVERT: B 411 MET cc_start: 0.8464 (mmt) cc_final: 0.7245 (tpp) REVERT: B 645 MET cc_start: 0.6343 (mmp) cc_final: 0.6053 (mmp) REVERT: C 50 MET cc_start: 0.7333 (ptt) cc_final: 0.6739 (ptt) REVERT: F 88 MET cc_start: -0.1900 (mmm) cc_final: -0.2813 (mmp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.6656 time to fit residues: 223.4421 Evaluate side-chains 204 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.431 ------------------------------------------------------------------------------- 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: 0.6980 chunk 159 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15254 Z= 0.168 Angle : 0.555 26.547 20678 Z= 0.291 Chirality : 0.037 0.151 2272 Planarity : 0.004 0.049 2582 Dihedral : 10.145 85.349 2309 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1778 helix: 0.87 (0.19), residues: 799 sheet: -0.48 (0.37), residues: 199 loop : -1.31 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 368 HIS 0.006 0.001 HIS C 110 PHE 0.015 0.002 PHE B 447 TYR 0.013 0.001 TYR A 110 ARG 0.005 0.000 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 242 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.304 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 581 MET cc_start: 0.7679 (mtm) cc_final: 0.6669 (mtm) REVERT: B 127 GLN cc_start: 0.7671 (mm-40) cc_final: 0.5814 (mt0) REVERT: B 306 ASN cc_start: 0.8191 (m110) cc_final: 0.7918 (m110) REVERT: C 23 THR cc_start: 0.8049 (p) cc_final: 0.7794 (p) REVERT: C 50 MET cc_start: 0.7520 (ptt) cc_final: 0.6800 (ptt) REVERT: F 88 MET cc_start: -0.1960 (mmm) cc_final: -0.3377 (mmp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.6614 time to fit residues: 230.1460 Evaluate side-chains 204 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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: 0.7980 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15254 Z= 0.280 Angle : 0.663 27.302 20678 Z= 0.361 Chirality : 0.039 0.166 2272 Planarity : 0.005 0.065 2582 Dihedral : 10.415 88.992 2309 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1778 helix: 0.42 (0.18), residues: 794 sheet: -0.64 (0.38), residues: 190 loop : -1.60 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 99 HIS 0.011 0.002 HIS B 649 PHE 0.021 0.002 PHE B 730 TYR 0.024 0.002 TYR F 83 ARG 0.010 0.001 ARG A 583 ********************** 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 237 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.359 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 581 MET cc_start: 0.7786 (mtm) cc_final: 0.7202 (mtm) REVERT: A 682 ASP cc_start: 0.7805 (t0) cc_final: 0.7139 (p0) REVERT: B 24 TYR cc_start: 0.8455 (m-10) cc_final: 0.8104 (m-80) REVERT: B 127 GLN cc_start: 0.7844 (mm-40) cc_final: 0.6255 (mt0) REVERT: B 179 MET cc_start: 0.6144 (mtm) cc_final: 0.5791 (mtm) REVERT: B 229 LYS cc_start: 0.8979 (tttp) cc_final: 0.8713 (ttmt) REVERT: B 263 CYS cc_start: 0.6743 (m) cc_final: 0.6274 (m) REVERT: B 645 MET cc_start: 0.6315 (mmp) cc_final: 0.6032 (mmp) REVERT: C 50 MET cc_start: 0.7381 (ptt) cc_final: 0.6702 (ptt) REVERT: F 88 MET cc_start: -0.1801 (mmm) cc_final: -0.2621 (mmp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.6506 time to fit residues: 220.9424 Evaluate side-chains 201 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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: 2.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 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 = 0.4252 r_free = 0.4252 target = 0.122515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.099819 restraints weight = 172459.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.104075 restraints weight = 94783.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.106988 restraints weight = 60148.160| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.8491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15254 Z= 0.238 Angle : 0.629 27.126 20678 Z= 0.336 Chirality : 0.038 0.158 2272 Planarity : 0.005 0.072 2582 Dihedral : 10.456 91.118 2309 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.05 (0.19), residues: 1778 helix: 0.30 (0.18), residues: 800 sheet: -0.67 (0.38), residues: 190 loop : -1.74 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 580 HIS 0.007 0.001 HIS B 634 PHE 0.018 0.002 PHE B 730 TYR 0.030 0.002 TYR B 620 ARG 0.022 0.001 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6558.28 seconds wall clock time: 116 minutes 43.30 seconds (7003.30 seconds total)