Starting phenix.real_space_refine on Mon Aug 25 15:05:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nki_12440/08_2025/7nki_12440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nki_12440/08_2025/7nki_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/cci-nas-00/data/ceres_data/7nki_12440/08_2025/7nki_12440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nki_12440/08_2025/7nki_12440.map" model { file = "/net/cci-nas-00/data/ceres_data/7nki_12440/08_2025/7nki_12440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nki_12440/08_2025/7nki_12440.cif" } resolution = 4.67 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.27, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 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: 2.89 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 5.39 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: 7.87 Time building geometry restraints manager: 3.99 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: 0.00 - 5.64: 52262 5.64 - 11.27: 3 11.27 - 16.91: 0 16.91 - 22.55: 1 22.55 - 28.19: 5 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 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.250 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: 0.160 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.020 ------------------------------------------------------------------------------- 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 15255 Z= 0.221 Angle : 0.671 26.918 20680 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 : 8.81 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.016 0.001 ARG F 70 TYR 0.152 0.004 TYR F 100 PHE 0.048 0.002 PHE A 446 TRP 0.026 0.001 TRP F 36 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00407 (15254) covalent geometry : angle 0.66958 (20678) SS BOND : bond 0.02818 ( 1) SS BOND : angle 3.80957 ( 2) hydrogen bonds : bond 0.14849 ( 731) hydrogen bonds : angle 5.98919 ( 2012) *********************** 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 to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.834 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: 0.3138 (tpp) REVERT: A 271 PRO cc_start: 0.6159 (Cg_endo) cc_final: 0.5667 (Cg_exo) REVERT: A 575 MET cc_start: 0.7816 (mtm) cc_final: 0.7509 (mtm) REVERT: A 581 MET cc_start: 0.7374 (mtp) cc_final: 0.6883 (mtp) REVERT: A 585 LEU cc_start: 0.8989 (mt) cc_final: 0.8706 (mm) REVERT: A 656 GLU cc_start: 0.6639 (mm-30) cc_final: 0.5781 (mm-30) REVERT: B 136 ASN cc_start: 0.8586 (m-40) cc_final: 0.8309 (m-40) REVERT: B 146 THR cc_start: 0.7925 (p) cc_final: 0.7711 (t) REVERT: B 344 PHE cc_start: 0.7674 (m-10) cc_final: 0.7320 (m-80) REVERT: B 413 ASN cc_start: 0.8254 (m110) cc_final: 0.7671 (p0) REVERT: B 528 THR cc_start: 0.7697 (m) cc_final: 0.6842 (p) REVERT: B 529 VAL cc_start: 0.9284 (t) cc_final: 0.8895 (p) REVERT: B 530 ILE cc_start: 0.8647 (mt) cc_final: 0.8363 (mt) REVERT: B 550 LEU cc_start: 0.7139 (mt) cc_final: 0.6881 (mt) REVERT: B 590 LEU cc_start: 0.5466 (mp) cc_final: 0.5242 (mt) REVERT: B 609 VAL cc_start: 0.4960 (t) cc_final: 0.4667 (t) REVERT: B 610 CYS cc_start: 0.7551 (m) cc_final: 0.6903 (t) REVERT: B 696 PHE cc_start: 0.7573 (t80) cc_final: 0.7224 (t80) REVERT: C 24 THR cc_start: 0.7797 (p) cc_final: 0.7501 (t) REVERT: F 88 MET cc_start: -0.1690 (mmm) cc_final: -0.3576 (mmp) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.3769 time to fit residues: 206.3338 Evaluate side-chains 269 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 676 ASN B 756 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.150948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.127055 restraints weight = 150445.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.133165 restraints weight = 79058.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.137173 restraints weight = 46468.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.139679 restraints weight = 29742.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.141550 restraints weight = 20891.873| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15255 Z= 0.161 Angle : 0.610 27.472 20680 Z= 0.326 Chirality : 0.039 0.149 2272 Planarity : 0.005 0.059 2582 Dihedral : 10.132 73.431 2309 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.19), residues: 1778 helix: 0.34 (0.18), residues: 796 sheet: -0.80 (0.38), residues: 187 loop : -1.08 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 124 TYR 0.017 0.001 TYR B 620 PHE 0.020 0.002 PHE A 446 TRP 0.018 0.001 TRP A 338 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00340 (15254) covalent geometry : angle 0.60961 (20678) SS BOND : bond 0.00439 ( 1) SS BOND : angle 0.87552 ( 2) hydrogen bonds : bond 0.04764 ( 731) hydrogen bonds : angle 5.06400 ( 2012) *********************** 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 301 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.789 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: A 360 MET cc_start: 0.9012 (mtp) cc_final: 0.8657 (mtp) REVERT: A 423 ILE cc_start: 0.5733 (pt) cc_final: 0.5432 (tp) REVERT: A 477 MET cc_start: 0.8921 (pmm) cc_final: 0.8549 (pmm) REVERT: A 575 MET cc_start: 0.8638 (mtm) cc_final: 0.8188 (mtm) REVERT: A 581 MET cc_start: 0.8309 (mtp) cc_final: 0.8020 (mtp) REVERT: A 682 ASP cc_start: 0.6771 (t0) cc_final: 0.6117 (t0) REVERT: A 713 HIS cc_start: 0.8488 (m-70) cc_final: 0.7816 (m-70) REVERT: B 246 MET cc_start: 0.7387 (tpp) cc_final: 0.6944 (tpp) REVERT: B 306 ASN cc_start: 0.6298 (m110) cc_final: 0.5658 (m110) REVERT: B 321 MET cc_start: 0.7243 (mtt) cc_final: 0.6740 (mtt) REVERT: B 409 MET cc_start: 0.7386 (ppp) cc_final: 0.6976 (ppp) REVERT: B 413 ASN cc_start: 0.8594 (m110) cc_final: 0.7713 (p0) REVERT: B 414 MET cc_start: 0.6567 (tpp) cc_final: 0.5903 (tpp) REVERT: B 610 CYS cc_start: 0.7918 (m) cc_final: 0.7340 (t) REVERT: B 620 TYR cc_start: 0.7207 (t80) cc_final: 0.6361 (t80) REVERT: C 1 MET cc_start: 0.5885 (mmm) cc_final: 0.4792 (mmm) REVERT: C 146 ASP cc_start: 0.8130 (p0) cc_final: 0.7197 (t0) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.3386 time to fit residues: 140.8902 Evaluate side-chains 242 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 85 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 162 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 425 ASN B 452 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.145634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.121885 restraints weight = 151429.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.127557 restraints weight = 80668.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.131327 restraints weight = 48077.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.133879 restraints weight = 31300.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.135602 restraints weight = 22044.072| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15255 Z= 0.156 Angle : 0.595 26.052 20680 Z= 0.321 Chirality : 0.038 0.149 2272 Planarity : 0.004 0.055 2582 Dihedral : 10.030 73.361 2309 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.19), residues: 1778 helix: 0.41 (0.18), residues: 806 sheet: -0.62 (0.37), residues: 191 loop : -1.21 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 238 TYR 0.031 0.002 TYR A 232 PHE 0.028 0.002 PHE A 223 TRP 0.010 0.001 TRP C 99 HIS 0.007 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00335 (15254) covalent geometry : angle 0.59461 (20678) SS BOND : bond 0.00328 ( 1) SS BOND : angle 0.76312 ( 2) hydrogen bonds : bond 0.04478 ( 731) hydrogen bonds : angle 4.90623 ( 2012) *********************** 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 270 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.762 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: A 360 MET cc_start: 0.8996 (mtp) cc_final: 0.8637 (mtp) REVERT: A 423 ILE cc_start: 0.5877 (pt) cc_final: 0.5637 (tp) REVERT: A 477 MET cc_start: 0.8951 (pmm) cc_final: 0.8559 (pmm) REVERT: A 575 MET cc_start: 0.8557 (mtm) cc_final: 0.8308 (mtm) REVERT: A 682 ASP cc_start: 0.7319 (t0) cc_final: 0.6574 (t0) REVERT: A 713 HIS cc_start: 0.8324 (m-70) cc_final: 0.7658 (m-70) REVERT: B 256 GLU cc_start: 0.9072 (tp30) cc_final: 0.8773 (tp30) REVERT: B 321 MET cc_start: 0.7063 (mtt) cc_final: 0.6850 (mtt) REVERT: C 23 THR cc_start: 0.9178 (m) cc_final: 0.8905 (p) REVERT: C 122 VAL cc_start: 0.3680 (t) cc_final: 0.2846 (t) REVERT: C 146 ASP cc_start: 0.8164 (p0) cc_final: 0.7588 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.3295 time to fit residues: 124.1688 Evaluate side-chains 219 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 120 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 425 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.140141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.116130 restraints weight = 157978.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.121609 restraints weight = 85370.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.125280 restraints weight = 51705.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.127805 restraints weight = 34155.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.129507 restraints weight = 24349.572| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15255 Z= 0.173 Angle : 0.608 27.666 20680 Z= 0.328 Chirality : 0.038 0.179 2272 Planarity : 0.005 0.100 2582 Dihedral : 10.048 73.402 2309 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.19), residues: 1778 helix: 0.47 (0.18), residues: 798 sheet: -0.58 (0.36), residues: 203 loop : -1.28 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 124 TYR 0.039 0.002 TYR A 232 PHE 0.018 0.002 PHE A 646 TRP 0.013 0.001 TRP C 99 HIS 0.020 0.002 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00370 (15254) covalent geometry : angle 0.60843 (20678) SS BOND : bond 0.00298 ( 1) SS BOND : angle 0.58885 ( 2) hydrogen bonds : bond 0.04358 ( 731) hydrogen bonds : angle 4.89201 ( 2012) *********************** 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 247 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8561 (t80) cc_final: 0.8351 (t80) REVERT: A 423 ILE cc_start: 0.6235 (pt) cc_final: 0.5854 (tp) REVERT: A 477 MET cc_start: 0.9043 (pmm) cc_final: 0.8599 (pmm) REVERT: A 682 ASP cc_start: 0.8117 (t0) cc_final: 0.7496 (t0) REVERT: A 707 PHE cc_start: 0.9203 (t80) cc_final: 0.8792 (t80) REVERT: B 321 MET cc_start: 0.7569 (mtt) cc_final: 0.7027 (mtt) REVERT: B 411 MET cc_start: 0.8064 (mmp) cc_final: 0.7527 (mmm) REVERT: B 413 ASN cc_start: 0.7742 (m-40) cc_final: 0.7373 (p0) REVERT: B 560 ARG cc_start: 0.8434 (mmt-90) cc_final: 0.7550 (mpt90) REVERT: B 579 LEU cc_start: 0.7848 (tp) cc_final: 0.7633 (tp) REVERT: B 696 PHE cc_start: 0.9190 (t80) cc_final: 0.8937 (t80) REVERT: C 1 MET cc_start: 0.6363 (mmm) cc_final: 0.6102 (mmm) REVERT: C 60 ASP cc_start: 0.7241 (m-30) cc_final: 0.6923 (m-30) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.3484 time to fit residues: 120.5809 Evaluate side-chains 213 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 107 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 161 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 452 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.137631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.113617 restraints weight = 155541.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118867 restraints weight = 82933.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.122554 restraints weight = 50399.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.125082 restraints weight = 33422.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.126738 restraints weight = 23986.773| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15255 Z= 0.162 Angle : 0.606 26.283 20680 Z= 0.323 Chirality : 0.038 0.152 2272 Planarity : 0.005 0.069 2582 Dihedral : 10.033 73.427 2309 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.19), residues: 1778 helix: 0.51 (0.18), residues: 797 sheet: -0.44 (0.38), residues: 190 loop : -1.33 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 233 TYR 0.034 0.002 TYR A 232 PHE 0.020 0.002 PHE A 191 TRP 0.012 0.001 TRP C 99 HIS 0.009 0.002 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00343 (15254) covalent geometry : angle 0.60640 (20678) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.52534 ( 2) hydrogen bonds : bond 0.04202 ( 731) hydrogen bonds : angle 4.83956 ( 2012) *********************** 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 to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 ILE cc_start: 0.6431 (pt) cc_final: 0.6177 (tp) REVERT: A 446 PHE cc_start: 0.8493 (m-10) cc_final: 0.8287 (m-10) REVERT: A 464 TYR cc_start: 0.7895 (t80) cc_final: 0.7654 (t80) REVERT: A 477 MET cc_start: 0.9049 (pmm) cc_final: 0.8616 (pmm) REVERT: A 682 ASP cc_start: 0.8615 (t0) cc_final: 0.8045 (t0) REVERT: B 162 ARG cc_start: 0.9268 (mtm180) cc_final: 0.8789 (ttp-110) REVERT: B 260 ARG cc_start: 0.8892 (tmt170) cc_final: 0.8302 (ptm-80) REVERT: B 321 MET cc_start: 0.7575 (mtt) cc_final: 0.7102 (mtt) REVERT: B 413 ASN cc_start: 0.7758 (m-40) cc_final: 0.7517 (p0) REVERT: B 414 MET cc_start: 0.6482 (tpp) cc_final: 0.6272 (tpp) REVERT: B 505 PHE cc_start: 0.7294 (t80) cc_final: 0.6827 (t80) REVERT: B 560 ARG cc_start: 0.8482 (mmt-90) cc_final: 0.7648 (mpt90) REVERT: C 60 ASP cc_start: 0.7250 (m-30) cc_final: 0.7007 (m-30) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3337 time to fit residues: 119.2470 Evaluate side-chains 212 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 135 optimal weight: 0.0670 chunk 177 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 641 ASN ** 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 = 0.4471 r_free = 0.4471 target = 0.139510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.115531 restraints weight = 153240.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.120868 restraints weight = 81824.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.124527 restraints weight = 49676.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.127049 restraints weight = 33145.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.128825 restraints weight = 23788.061| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15255 Z= 0.110 Angle : 0.553 26.182 20680 Z= 0.290 Chirality : 0.037 0.151 2272 Planarity : 0.004 0.057 2582 Dihedral : 9.881 75.693 2309 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.19), residues: 1778 helix: 0.89 (0.18), residues: 792 sheet: -0.48 (0.36), residues: 212 loop : -1.15 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 124 TYR 0.043 0.001 TYR A 232 PHE 0.021 0.001 PHE A 236 TRP 0.010 0.001 TRP B 580 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00245 (15254) covalent geometry : angle 0.55291 (20678) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.32450 ( 2) hydrogen bonds : bond 0.03888 ( 731) hydrogen bonds : angle 4.58508 ( 2012) *********************** 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 242 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8618 (tpp) cc_final: 0.8409 (mmm) REVERT: A 276 CYS cc_start: 0.7330 (m) cc_final: 0.7102 (p) REVERT: A 423 ILE cc_start: 0.6455 (pt) cc_final: 0.6077 (tp) REVERT: A 464 TYR cc_start: 0.8020 (t80) cc_final: 0.7757 (t80) REVERT: A 477 MET cc_start: 0.8990 (pmm) cc_final: 0.8517 (pmm) REVERT: A 575 MET cc_start: 0.8450 (ttm) cc_final: 0.7914 (tpp) REVERT: A 682 ASP cc_start: 0.8523 (t0) cc_final: 0.8052 (t0) REVERT: B 162 ARG cc_start: 0.9266 (mtm180) cc_final: 0.8785 (ttp-110) REVERT: B 260 ARG cc_start: 0.8861 (tmt170) cc_final: 0.8241 (ptm-80) REVERT: B 321 MET cc_start: 0.7462 (mtt) cc_final: 0.6955 (mtt) REVERT: B 413 ASN cc_start: 0.7751 (m-40) cc_final: 0.7341 (p0) REVERT: C 60 ASP cc_start: 0.6973 (m-30) cc_final: 0.6756 (m-30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3043 time to fit residues: 104.9871 Evaluate side-chains 205 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 425 ASN B 582 GLN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.128511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.105070 restraints weight = 163004.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.109766 restraints weight = 88975.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.113018 restraints weight = 55398.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.115230 restraints weight = 38030.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.116765 restraints weight = 28382.656| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 15255 Z= 0.226 Angle : 0.695 27.408 20680 Z= 0.378 Chirality : 0.040 0.195 2272 Planarity : 0.005 0.076 2582 Dihedral : 10.283 79.920 2309 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.19), residues: 1778 helix: 0.27 (0.18), residues: 799 sheet: -0.69 (0.38), residues: 199 loop : -1.58 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 583 TYR 0.035 0.003 TYR A 232 PHE 0.023 0.002 PHE B 333 TRP 0.074 0.003 TRP A 368 HIS 0.010 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00468 (15254) covalent geometry : angle 0.69530 (20678) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.53686 ( 2) hydrogen bonds : bond 0.04596 ( 731) hydrogen bonds : angle 5.15966 ( 2012) *********************** 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 235 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 TYR cc_start: 0.8318 (t80) cc_final: 0.7938 (t80) REVERT: A 477 MET cc_start: 0.9040 (pmm) cc_final: 0.8558 (pmm) REVERT: A 575 MET cc_start: 0.8745 (ttm) cc_final: 0.8225 (tpp) REVERT: A 682 ASP cc_start: 0.9074 (t0) cc_final: 0.8789 (t0) REVERT: B 162 ARG cc_start: 0.9318 (mtm180) cc_final: 0.8831 (ttp-110) REVERT: B 229 LYS cc_start: 0.8974 (tttp) cc_final: 0.8720 (ttmt) REVERT: B 260 ARG cc_start: 0.8956 (tmt170) cc_final: 0.8370 (ptm-80) REVERT: B 321 MET cc_start: 0.7871 (mtt) cc_final: 0.7408 (mtt) REVERT: B 409 MET cc_start: 0.7439 (ppp) cc_final: 0.6392 (ppp) REVERT: B 411 MET cc_start: 0.7633 (mmp) cc_final: 0.7088 (mmt) REVERT: B 412 PHE cc_start: 0.7967 (m-10) cc_final: 0.7676 (m-10) REVERT: B 560 ARG cc_start: 0.8669 (mmt-90) cc_final: 0.7506 (mpt90) REVERT: C 202 MET cc_start: 0.7854 (mmm) cc_final: 0.7419 (mmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2831 time to fit residues: 94.5939 Evaluate side-chains 205 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 294 GLN B 328 ASN B 425 ASN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.132110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.108955 restraints weight = 161023.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.113713 restraints weight = 87063.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.117042 restraints weight = 53925.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.119347 restraints weight = 36734.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.120880 restraints weight = 26970.084| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15255 Z= 0.134 Angle : 0.590 26.860 20680 Z= 0.314 Chirality : 0.038 0.151 2272 Planarity : 0.005 0.068 2582 Dihedral : 10.196 81.204 2309 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 1778 helix: 0.56 (0.18), residues: 806 sheet: -0.56 (0.38), residues: 200 loop : -1.50 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 334 TYR 0.029 0.002 TYR A 232 PHE 0.019 0.002 PHE B 333 TRP 0.032 0.002 TRP A 368 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00296 (15254) covalent geometry : angle 0.59036 (20678) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.39023 ( 2) hydrogen bonds : bond 0.04135 ( 731) hydrogen bonds : angle 4.79879 ( 2012) *********************** 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 241 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.846 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: A 1 MET cc_start: 0.4405 (mmp) cc_final: 0.4159 (mmp) REVERT: A 464 TYR cc_start: 0.8212 (t80) cc_final: 0.7834 (t80) REVERT: A 465 ILE cc_start: 0.9021 (mm) cc_final: 0.8770 (pt) REVERT: A 477 MET cc_start: 0.9006 (pmm) cc_final: 0.8497 (pmm) REVERT: A 575 MET cc_start: 0.8656 (ttm) cc_final: 0.8085 (tpp) REVERT: A 682 ASP cc_start: 0.8981 (t0) cc_final: 0.8766 (t0) REVERT: B 162 ARG cc_start: 0.9309 (mtm180) cc_final: 0.8824 (ttp-110) REVERT: B 229 LYS cc_start: 0.8856 (tttp) cc_final: 0.8652 (ttmt) REVERT: B 260 ARG cc_start: 0.8943 (tmt170) cc_final: 0.8307 (ptm-80) REVERT: B 321 MET cc_start: 0.7726 (mtt) cc_final: 0.7220 (mtt) REVERT: B 412 PHE cc_start: 0.7842 (m-10) cc_final: 0.7608 (m-10) REVERT: B 579 LEU cc_start: 0.7894 (tp) cc_final: 0.7671 (tp) REVERT: B 620 TYR cc_start: 0.8279 (t80) cc_final: 0.7514 (t80) REVERT: C 60 ASP cc_start: 0.7062 (m-30) cc_final: 0.6847 (m-30) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3439 time to fit residues: 116.9980 Evaluate side-chains 213 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 425 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.124569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.100855 restraints weight = 168030.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.105526 restraints weight = 91143.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.108711 restraints weight = 56834.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.110938 restraints weight = 39331.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.112467 restraints weight = 29477.199| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15255 Z= 0.197 Angle : 0.665 27.036 20680 Z= 0.358 Chirality : 0.039 0.158 2272 Planarity : 0.005 0.074 2582 Dihedral : 10.467 85.505 2309 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1778 helix: 0.25 (0.18), residues: 806 sheet: -0.66 (0.38), residues: 195 loop : -1.74 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 583 TYR 0.034 0.002 TYR B 82 PHE 0.019 0.002 PHE B 730 TRP 0.021 0.002 TRP C 99 HIS 0.012 0.002 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00418 (15254) covalent geometry : angle 0.66465 (20678) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.43214 ( 2) hydrogen bonds : bond 0.04350 ( 731) hydrogen bonds : angle 5.16116 ( 2012) *********************** 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 247 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 TYR cc_start: 0.8222 (t80) cc_final: 0.7887 (t80) REVERT: A 465 ILE cc_start: 0.9105 (mm) cc_final: 0.8852 (pt) REVERT: A 477 MET cc_start: 0.9092 (pmm) cc_final: 0.8605 (pmm) REVERT: A 575 MET cc_start: 0.8320 (ttm) cc_final: 0.7947 (tpp) REVERT: B 229 LYS cc_start: 0.8439 (tttp) cc_final: 0.8116 (ttmt) REVERT: B 260 ARG cc_start: 0.9030 (tmt170) cc_final: 0.8552 (ptm-80) REVERT: B 321 MET cc_start: 0.7875 (mtt) cc_final: 0.7337 (mtt) REVERT: B 412 PHE cc_start: 0.8171 (m-10) cc_final: 0.7898 (m-10) REVERT: B 481 LYS cc_start: 0.8797 (mttm) cc_final: 0.8187 (mtmm) REVERT: B 507 MET cc_start: 0.8441 (mmm) cc_final: 0.8062 (mmm) REVERT: B 560 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.6995 (mpt90) REVERT: B 579 LEU cc_start: 0.7963 (tp) cc_final: 0.7732 (tp) REVERT: B 620 TYR cc_start: 0.8289 (t80) cc_final: 0.7979 (t80) REVERT: C 47 MET cc_start: 0.7995 (tpp) cc_final: 0.7589 (tpp) REVERT: C 60 ASP cc_start: 0.7471 (m-30) cc_final: 0.7250 (m-30) REVERT: C 202 MET cc_start: 0.8218 (mmm) cc_final: 0.8009 (mmm) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3440 time to fit residues: 120.3955 Evaluate side-chains 210 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.126824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.102408 restraints weight = 166350.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.107334 restraints weight = 89498.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.110720 restraints weight = 55357.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.113030 restraints weight = 37967.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.114627 restraints weight = 28301.621| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.7712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15255 Z= 0.118 Angle : 0.589 27.022 20680 Z= 0.308 Chirality : 0.038 0.157 2272 Planarity : 0.005 0.067 2582 Dihedral : 10.297 86.649 2309 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.19), residues: 1778 helix: 0.66 (0.18), residues: 805 sheet: -0.46 (0.38), residues: 195 loop : -1.54 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 498 TYR 0.029 0.002 TYR A 232 PHE 0.065 0.002 PHE A 446 TRP 0.022 0.001 TRP A 368 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00260 (15254) covalent geometry : angle 0.58900 (20678) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.42573 ( 2) hydrogen bonds : bond 0.03886 ( 731) hydrogen bonds : angle 4.81761 ( 2012) ********************** 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 248 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.873 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 374 MET cc_start: 0.8592 (mtt) cc_final: 0.8024 (mtt) REVERT: A 465 ILE cc_start: 0.9189 (mm) cc_final: 0.8854 (pt) REVERT: A 477 MET cc_start: 0.9111 (pmm) cc_final: 0.8583 (pmm) REVERT: A 581 MET cc_start: 0.8134 (mtm) cc_final: 0.7185 (mtm) REVERT: B 229 LYS cc_start: 0.8178 (tttp) cc_final: 0.7777 (ttmt) REVERT: B 260 ARG cc_start: 0.9005 (tmt170) cc_final: 0.8409 (ptm-80) REVERT: B 263 CYS cc_start: 0.6773 (m) cc_final: 0.6191 (m) REVERT: B 412 PHE cc_start: 0.8154 (m-10) cc_final: 0.7873 (m-10) REVERT: B 507 MET cc_start: 0.8428 (mmm) cc_final: 0.8064 (mmm) REVERT: B 560 ARG cc_start: 0.7918 (mmt-90) cc_final: 0.7577 (mpt180) REVERT: B 579 LEU cc_start: 0.7986 (tp) cc_final: 0.7757 (tp) REVERT: B 620 TYR cc_start: 0.8332 (t80) cc_final: 0.7485 (t80) REVERT: C 60 ASP cc_start: 0.6992 (m-30) cc_final: 0.6752 (m-30) REVERT: C 202 MET cc_start: 0.8199 (mmm) cc_final: 0.7910 (mmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3277 time to fit residues: 116.7992 Evaluate side-chains 215 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 86 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.125781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.101773 restraints weight = 168889.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.106482 restraints weight = 91165.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.109746 restraints weight = 56879.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.111937 restraints weight = 39418.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.113513 restraints weight = 29743.276| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.7952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15255 Z= 0.148 Angle : 0.599 27.050 20680 Z= 0.316 Chirality : 0.038 0.150 2272 Planarity : 0.005 0.062 2582 Dihedral : 10.316 88.026 2309 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.19), residues: 1778 helix: 0.66 (0.18), residues: 799 sheet: -0.48 (0.38), residues: 195 loop : -1.52 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 498 TYR 0.029 0.002 TYR A 232 PHE 0.046 0.002 PHE A 446 TRP 0.020 0.002 TRP A 368 HIS 0.005 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00311 (15254) covalent geometry : angle 0.59870 (20678) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.37168 ( 2) hydrogen bonds : bond 0.03935 ( 731) hydrogen bonds : angle 4.91629 ( 2012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.01 seconds wall clock time: 95 minutes 56.76 seconds (5756.76 seconds total)