Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 06:30:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/08_2023/7nki_12440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/08_2023/7nki_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_12440/08_2023/7nki_12440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/08_2023/7nki_12440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/08_2023/7nki_12440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nki_12440/08_2023/7nki_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-1.21rc1-5044/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: 12.44, 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: 23.51 Conformation dependent library (CDL) restraints added in 2.6 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: 13.04 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: 11.44 Time building geometry restraints manager: 24.09 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: 10953 17.94 - 35.89: 727 35.89 - 53.83: 139 53.83 - 71.77: 37 71.77 - 89.72: 11 Dihedral angle restraints: 11867 sinusoidal: 5814 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 11864 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.470 Extract box with map and model: 3.830 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 99.450 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.150 ------------------------------------------------------------------------------- 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 : 13.486 89.718 5891 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 % 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 *********************** 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 : 3.264 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.7386 time to fit residues: 406.8530 Evaluate side-chains 262 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0649 ------------------------------------------------------------------------------- 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: 4.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN B 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4698 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 15254 Z= 0.198 Angle : 0.581 27.395 20678 Z= 0.308 Chirality : 0.038 0.148 2272 Planarity : 0.004 0.048 2582 Dihedral : 6.634 61.044 2231 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1778 helix: 0.43 (0.18), residues: 795 sheet: -0.81 (0.36), residues: 202 loop : -1.07 (0.21), residues: 781 *********************** 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 292 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.539 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.7647 time to fit residues: 310.7694 Evaluate side-chains 239 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0254 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 756 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4865 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15254 Z= 0.191 Angle : 0.570 26.325 20678 Z= 0.304 Chirality : 0.037 0.148 2272 Planarity : 0.004 0.044 2582 Dihedral : 6.578 64.135 2231 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.00 % 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: -0.46 (0.19), residues: 1778 helix: 0.56 (0.18), residues: 798 sheet: -0.68 (0.36), residues: 199 loop : -1.05 (0.21), residues: 781 *********************** 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 275 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.372 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 outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.7210 time to fit residues: 275.9037 Evaluate side-chains 228 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2543 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 HIS ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS F 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5163 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 15254 Z= 0.238 Angle : 0.604 28.118 20678 Z= 0.322 Chirality : 0.038 0.166 2272 Planarity : 0.004 0.057 2582 Dihedral : 6.746 70.269 2231 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.06 % 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: -0.50 (0.19), residues: 1778 helix: 0.53 (0.18), residues: 800 sheet: -0.45 (0.36), residues: 205 loop : -1.17 (0.21), residues: 773 *********************** 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 266 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 2.453 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 outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.6799 time to fit residues: 256.3613 Evaluate side-chains 216 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9699 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN B 292 ASN B 294 GLN B 313 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 15254 Z= 0.402 Angle : 0.805 25.618 20678 Z= 0.445 Chirality : 0.042 0.186 2272 Planarity : 0.007 0.066 2582 Dihedral : 7.552 75.265 2231 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 28.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.75 % Favored : 93.08 % Rotamer Outliers : 0.06 % 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: -1.66 (0.18), residues: 1778 helix: -0.45 (0.17), residues: 799 sheet: -0.87 (0.37), residues: 192 loop : -1.79 (0.19), residues: 787 *********************** 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 254 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.417 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 outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.6982 time to fit residues: 251.4041 Evaluate side-chains 211 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4055 time to fit residues: 3.6857 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 670 GLN ** 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** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 15254 Z= 0.216 Angle : 0.605 26.887 20678 Z= 0.325 Chirality : 0.038 0.154 2272 Planarity : 0.005 0.058 2582 Dihedral : 7.138 77.959 2231 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.00 % 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: -1.09 (0.19), residues: 1778 helix: 0.17 (0.18), residues: 799 sheet: -0.74 (0.37), residues: 199 loop : -1.63 (0.20), residues: 780 *********************** 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 250 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.626 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 outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.6850 time to fit residues: 244.9097 Evaluate side-chains 205 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7786 ------------------------------------------------------------------------------- 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: 8.9990 chunk 125 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 276 ASN B 284 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.7442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 15254 Z= 0.386 Angle : 0.771 26.895 20678 Z= 0.425 Chirality : 0.041 0.155 2272 Planarity : 0.006 0.063 2582 Dihedral : 7.532 82.449 2231 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 30.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.66 % Favored : 91.28 % Rotamer Outliers : 0.00 % 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: -1.84 (0.18), residues: 1778 helix: -0.55 (0.17), residues: 800 sheet: -0.96 (0.36), residues: 190 loop : -1.95 (0.20), residues: 788 *********************** 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 239 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.295 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 outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.6575 time to fit residues: 224.1828 Evaluate side-chains 199 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9957 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 466 ASN B 16 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.8630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 15254 Z= 0.370 Angle : 0.786 27.840 20678 Z= 0.433 Chirality : 0.043 0.187 2272 Planarity : 0.007 0.078 2582 Dihedral : 7.958 88.105 2231 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 32.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 0.06 % 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: -2.47 (0.18), residues: 1778 helix: -1.04 (0.16), residues: 815 sheet: -1.24 (0.36), residues: 188 loop : -2.35 (0.20), residues: 775 *********************** 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 243 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.481 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 outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.6496 time to fit residues: 227.3301 Evaluate side-chains 205 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1425 ------------------------------------------------------------------------------- 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: 9.9990 chunk 164 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.8672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 15254 Z= 0.186 Angle : 0.614 27.546 20678 Z= 0.323 Chirality : 0.038 0.158 2272 Planarity : 0.005 0.057 2582 Dihedral : 7.398 89.086 2231 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.00 % 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: -1.48 (0.19), residues: 1778 helix: -0.08 (0.17), residues: 809 sheet: -0.98 (0.36), residues: 193 loop : -1.94 (0.21), residues: 776 *********************** 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 236 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.382 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 outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.6306 time to fit residues: 215.3838 Evaluate side-chains 199 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1245 ------------------------------------------------------------------------------- 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: 2.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 533 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.8972 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= 0.226 Angle : 0.620 27.170 20678 Z= 0.333 Chirality : 0.038 0.149 2272 Planarity : 0.005 0.059 2582 Dihedral : 7.515 91.468 2231 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.00 % 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: -1.45 (0.19), residues: 1778 helix: -0.04 (0.18), residues: 809 sheet: -0.87 (0.37), residues: 188 loop : -1.96 (0.21), residues: 781 ********************** 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 229 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.498 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 outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.6557 time to fit residues: 218.1675 Evaluate side-chains 197 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1023 ------------------------------------------------------------------------------- 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: 0.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.121630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.098737 restraints weight = 170516.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.103063 restraints weight = 93659.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.106005 restraints weight = 59460.096| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 15254 Z= 0.212 Angle : 0.620 27.232 20678 Z= 0.329 Chirality : 0.038 0.152 2272 Planarity : 0.005 0.054 2582 Dihedral : 7.438 92.758 2231 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.00 % 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: -1.26 (0.19), residues: 1778 helix: 0.13 (0.18), residues: 808 sheet: -0.85 (0.37), residues: 193 loop : -1.87 (0.21), residues: 777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6383.94 seconds wall clock time: 114 minutes 33.95 seconds (6873.95 seconds total)