Starting phenix.real_space_refine on Mon Aug 25 14:57:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nka_12435/08_2025/7nka_12435.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nka_12435/08_2025/7nka_12435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nka_12435/08_2025/7nka_12435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nka_12435/08_2025/7nka_12435.map" model { file = "/net/cci-nas-00/data/ceres_data/7nka_12435/08_2025/7nka_12435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nka_12435/08_2025/7nka_12435.cif" } resolution = 4.07 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= 0.015 sd= 0.212 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 106 5.16 5 C 9303 2.51 5 N 2599 2.21 5 O 2879 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: 28778 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: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 729 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 3 Time building chain proxies: 5.33, per 1000 atoms: 0.19 Number of scatterers: 28778 At special positions: 0 Unit cell: (100.8, 113.4, 176.4, 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 106 16.00 P 23 15.00 O 2879 8.00 N 2599 7.00 C 9303 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 95 " distance=2.01 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: 2.00 Conformation dependent library (CDL) restraints added in 883.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 17 sheets defined 49.6% alpha, 14.3% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.59 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: 3.691A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.947A 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: 4.634A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.973A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.778A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.826A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.587A 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: 3.509A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A 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: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.330A 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: 3.977A 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: 3.892A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.236A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.524A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.658A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.618A 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 86 through 90 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: 4.136A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A 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: 11.690A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.065A 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: 4.612A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.035A 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: 3.517A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.514A 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: 6.635A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.521A 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: 5.972A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.504A pdb=" N GLY F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) 728 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: 6.30 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13841 1.03 - 1.23: 262 1.23 - 1.43: 6173 1.43 - 1.63: 8663 1.63 - 1.82: 183 Bond restraints: 29122 Sorted by residual: bond pdb=" CD ARG F 50 " pdb=" NE ARG F 50 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.40e-02 5.10e+03 6.59e+00 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.40e-02 5.10e+03 6.53e+00 bond pdb=" C GLU A 677 " pdb=" O GLU A 677 " ideal model delta sigma weight residual 1.235 1.223 0.012 4.70e-03 4.53e+04 6.42e+00 bond pdb=" CD ARG F 66 " pdb=" NE ARG F 66 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.40e-02 5.10e+03 6.36e+00 ... (remaining 29117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52262 5.65 - 11.30: 3 11.30 - 16.95: 0 16.95 - 22.60: 1 22.60 - 28.25: 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 79.75 28.25 3.00e+00 1.11e-01 8.86e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.38 27.62 3.00e+00 1.11e-01 8.47e+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 81.88 27.12 3.00e+00 1.11e-01 8.17e+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 82.41 26.59 3.00e+00 1.11e-01 7.86e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.76 -26.86 3.20e+00 9.77e-02 7.04e+01 ... (remaining 52266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12580 17.93 - 35.86: 847 35.86 - 53.79: 257 53.79 - 71.72: 85 71.72 - 89.66: 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 -155.06 -24.94 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 180.00 158.40 21.60 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 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 13783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1941 0.055 - 0.110: 268 0.110 - 0.165: 53 0.165 - 0.221: 12 0.221 - 0.276: 1 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA THR F 77 " pdb=" N THR F 77 " pdb=" C THR F 77 " pdb=" CB THR F 77 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN F 76 " pdb=" N ASN F 76 " pdb=" C ASN F 76 " pdb=" CB ASN F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP F 65 " pdb=" N ASP F 65 " pdb=" C ASP F 65 " pdb=" CB ASP F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.61e-01 ... (remaining 2272 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 67 " 0.039 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE F 67 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE F 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE F 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE F 67 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE F 67 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE F 67 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.031 2.00e-02 2.50e+03 2.04e-02 8.35e+00 pdb=" CG TYR F 37 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 36 " -0.021 2.00e-02 2.50e+03 1.81e-02 8.15e+00 pdb=" CG TRP F 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP F 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 36 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 36 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP F 36 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP F 36 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 36 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 36 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP F 36 " -0.006 2.00e-02 2.50e+03 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1258 2.17 - 2.78: 56204 2.78 - 3.39: 80859 3.39 - 3.99: 105796 3.99 - 4.60: 165064 Nonbonded interactions: 409181 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.567 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 1.596 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409176 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 29.000 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5127 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 0.048 15255 Z= 0.222 Angle : 0.672 26.857 20680 Z= 0.393 Chirality : 0.043 0.276 2275 Planarity : 0.005 0.085 2584 Dihedral : 14.258 89.655 5967 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 1780 helix: 0.45 (0.19), residues: 786 sheet: -0.64 (0.37), residues: 184 loop : -1.23 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 66 TYR 0.033 0.002 TYR F 37 PHE 0.048 0.002 PHE A 446 TRP 0.030 0.002 TRP F 36 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00407 (15254) covalent geometry : angle 0.67122 (20678) SS BOND : bond 0.02132 ( 1) SS BOND : angle 2.84168 ( 2) hydrogen bonds : bond 0.14886 ( 733) hydrogen bonds : angle 5.96230 ( 2012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 502 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.563 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: A 257 ILE cc_start: 0.6131 (mt) cc_final: 0.5690 (mt) REVERT: A 272 ASP cc_start: 0.6141 (m-30) cc_final: 0.4867 (t0) REVERT: A 523 MET cc_start: 0.6118 (mtt) cc_final: 0.5332 (mtt) REVERT: A 602 VAL cc_start: 0.6611 (t) cc_final: 0.6282 (t) REVERT: B 132 THR cc_start: 0.6969 (m) cc_final: 0.6714 (m) REVERT: B 141 THR cc_start: 0.7205 (m) cc_final: 0.6991 (m) REVERT: B 218 LEU cc_start: 0.6427 (mt) cc_final: 0.6199 (tt) REVERT: B 277 GLU cc_start: 0.7326 (mp0) cc_final: 0.6792 (mm-30) REVERT: B 317 MET cc_start: 0.5153 (mmm) cc_final: 0.4524 (tpp) REVERT: B 417 THR cc_start: 0.7801 (m) cc_final: 0.7533 (m) REVERT: B 517 ILE cc_start: 0.7955 (mm) cc_final: 0.7626 (mm) REVERT: B 535 ILE cc_start: 0.6259 (mt) cc_final: 0.6003 (mt) REVERT: B 608 GLU cc_start: 0.6779 (tt0) cc_final: 0.6028 (pm20) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.2833 time to fit residues: 199.6780 Evaluate side-chains 322 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 326 HIS A 437 HIS B 314 ASN B 425 ASN C 27 HIS F 5 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.205087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172667 restraints weight = 74407.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178858 restraints weight = 34511.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182652 restraints weight = 19752.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.185073 restraints weight = 13261.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.186321 restraints weight = 10121.713| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15255 Z= 0.161 Angle : 0.617 27.340 20680 Z= 0.325 Chirality : 0.040 0.156 2275 Planarity : 0.005 0.054 2584 Dihedral : 10.150 73.295 2308 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % 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: -0.63 (0.19), residues: 1780 helix: 0.37 (0.18), residues: 792 sheet: -0.44 (0.37), residues: 195 loop : -1.17 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 216 TYR 0.020 0.002 TYR C 115 PHE 0.022 0.002 PHE A 446 TRP 0.023 0.001 TRP A 368 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00354 (15254) covalent geometry : angle 0.61740 (20678) SS BOND : bond 0.00397 ( 1) SS BOND : angle 1.13259 ( 2) hydrogen bonds : bond 0.04872 ( 733) hydrogen bonds : angle 4.96847 ( 2012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 371 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.494 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: A 86 MET cc_start: 0.7337 (tpt) cc_final: 0.6809 (tpt) REVERT: A 155 MET cc_start: 0.5853 (tmm) cc_final: 0.4967 (tmm) REVERT: A 272 ASP cc_start: 0.7110 (m-30) cc_final: 0.5524 (t0) REVERT: A 523 MET cc_start: 0.5895 (mtt) cc_final: 0.5231 (mtt) REVERT: A 548 MET cc_start: 0.6377 (ttt) cc_final: 0.6084 (ttt) REVERT: B 3 VAL cc_start: 0.7538 (t) cc_final: 0.7223 (t) REVERT: B 174 MET cc_start: 0.8342 (mmt) cc_final: 0.8138 (tpp) REVERT: B 218 LEU cc_start: 0.7766 (mt) cc_final: 0.7381 (tp) REVERT: B 277 GLU cc_start: 0.7878 (mp0) cc_final: 0.7221 (mm-30) REVERT: B 608 GLU cc_start: 0.7278 (tt0) cc_final: 0.5987 (pm20) REVERT: B 609 VAL cc_start: 0.7463 (t) cc_final: 0.7124 (t) REVERT: B 655 MET cc_start: 0.8486 (ttm) cc_final: 0.8251 (ttm) REVERT: C 20 LEU cc_start: 0.8605 (mt) cc_final: 0.8385 (mm) REVERT: C 66 MET cc_start: 0.5168 (mmm) cc_final: 0.4941 (mtt) REVERT: C 196 CYS cc_start: 0.7211 (m) cc_final: 0.6658 (m) REVERT: C 206 MET cc_start: 0.7847 (tpp) cc_final: 0.7627 (tpp) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.2568 time to fit residues: 138.8084 Evaluate side-chains 275 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 156 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS B 134 ASN B 310 ASN B 425 ASN B 756 GLN C 27 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.201536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168240 restraints weight = 74623.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174327 restraints weight = 35536.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178178 restraints weight = 20590.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.180223 restraints weight = 13879.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.181860 restraints weight = 10832.358| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15255 Z= 0.128 Angle : 0.553 26.145 20680 Z= 0.291 Chirality : 0.038 0.159 2275 Planarity : 0.004 0.046 2584 Dihedral : 10.012 73.344 2308 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.13 % Allowed : 1.76 % Favored : 98.11 % 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: -0.44 (0.19), residues: 1780 helix: 0.53 (0.18), residues: 792 sheet: -0.27 (0.36), residues: 202 loop : -1.10 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 101 TYR 0.023 0.001 TYR B 217 PHE 0.021 0.001 PHE A 446 TRP 0.008 0.001 TRP B 613 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00280 (15254) covalent geometry : angle 0.55271 (20678) SS BOND : bond 0.00641 ( 1) SS BOND : angle 0.85436 ( 2) hydrogen bonds : bond 0.04419 ( 733) hydrogen bonds : angle 4.70461 ( 2012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 338 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 0.610 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: A 86 MET cc_start: 0.7496 (tpt) cc_final: 0.7070 (tpp) REVERT: A 155 MET cc_start: 0.5884 (tmm) cc_final: 0.4991 (tmm) REVERT: A 204 ARG cc_start: 0.6649 (tmm-80) cc_final: 0.6442 (tmm-80) REVERT: A 272 ASP cc_start: 0.7325 (m-30) cc_final: 0.5881 (t0) REVERT: A 523 MET cc_start: 0.6115 (mtt) cc_final: 0.5636 (mtt) REVERT: A 536 LYS cc_start: 0.6363 (ttpt) cc_final: 0.5374 (ttpt) REVERT: A 548 MET cc_start: 0.6444 (ttt) cc_final: 0.6193 (ttt) REVERT: A 597 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6631 (mt-10) REVERT: B 3 VAL cc_start: 0.7663 (t) cc_final: 0.7374 (t) REVERT: B 52 LYS cc_start: 0.6826 (mtmt) cc_final: 0.6342 (tppt) REVERT: B 218 LEU cc_start: 0.7635 (mt) cc_final: 0.7409 (tp) REVERT: B 277 GLU cc_start: 0.7880 (mp0) cc_final: 0.7375 (mm-30) REVERT: B 321 MET cc_start: 0.6742 (mtm) cc_final: 0.6487 (ttm) REVERT: B 476 ASN cc_start: 0.8189 (m-40) cc_final: 0.7965 (m-40) REVERT: B 480 LYS cc_start: 0.6680 (mmtm) cc_final: 0.6176 (mtmm) REVERT: B 608 GLU cc_start: 0.7046 (tt0) cc_final: 0.5901 (pm20) REVERT: B 609 VAL cc_start: 0.7516 (t) cc_final: 0.7264 (t) REVERT: C 20 LEU cc_start: 0.8613 (mt) cc_final: 0.8410 (mm) REVERT: C 47 MET cc_start: 0.8854 (tpp) cc_final: 0.8512 (tpp) REVERT: C 64 MET cc_start: 0.7446 (ttm) cc_final: 0.7219 (ttm) REVERT: F 96 ASN cc_start: 0.7782 (t0) cc_final: 0.7325 (m-40) outliers start: 2 outliers final: 1 residues processed: 337 average time/residue: 0.2547 time to fit residues: 125.7785 Evaluate side-chains 273 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 40.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN B 294 GLN B 425 ASN B 537 ASN B 605 HIS B 654 ASN B 664 HIS C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.184881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147416 restraints weight = 75673.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153045 restraints weight = 37535.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156652 restraints weight = 22836.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158920 restraints weight = 16104.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.160130 restraints weight = 12753.778| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 15255 Z= 0.216 Angle : 0.687 28.601 20680 Z= 0.365 Chirality : 0.042 0.263 2275 Planarity : 0.006 0.094 2584 Dihedral : 10.195 75.845 2308 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % 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: -0.87 (0.19), residues: 1780 helix: 0.18 (0.18), residues: 800 sheet: -0.23 (0.36), residues: 197 loop : -1.42 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 174 TYR 0.031 0.002 TYR C 55 PHE 0.034 0.003 PHE A 520 TRP 0.016 0.002 TRP B 438 HIS 0.009 0.002 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00483 (15254) covalent geometry : angle 0.68675 (20678) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.47668 ( 2) hydrogen bonds : bond 0.05216 ( 733) hydrogen bonds : angle 5.07124 ( 2012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 313 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.504 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: A 86 MET cc_start: 0.7806 (tpt) cc_final: 0.7219 (tpp) REVERT: A 155 MET cc_start: 0.5446 (tmm) cc_final: 0.4633 (tmm) REVERT: A 272 ASP cc_start: 0.7783 (m-30) cc_final: 0.6203 (t0) REVERT: A 545 ILE cc_start: 0.8264 (pt) cc_final: 0.7888 (tp) REVERT: A 597 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7037 (mm-30) REVERT: B 218 LEU cc_start: 0.7950 (mt) cc_final: 0.7566 (tp) REVERT: B 277 GLU cc_start: 0.8159 (mp0) cc_final: 0.7485 (mm-30) REVERT: B 321 MET cc_start: 0.6731 (mtm) cc_final: 0.6472 (ttm) REVERT: B 480 LYS cc_start: 0.7299 (mmtm) cc_final: 0.6597 (mtmm) REVERT: B 507 MET cc_start: 0.8886 (mtp) cc_final: 0.8686 (mtp) REVERT: B 608 GLU cc_start: 0.7177 (tt0) cc_final: 0.6653 (pm20) REVERT: C 64 MET cc_start: 0.7474 (ttm) cc_final: 0.7265 (ttm) REVERT: C 66 MET cc_start: 0.6318 (mmm) cc_final: 0.6061 (mtt) REVERT: F 96 ASN cc_start: 0.7991 (t0) cc_final: 0.7675 (t0) outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 0.2507 time to fit residues: 112.8672 Evaluate side-chains 251 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 306 ASN B 425 ASN B 476 ASN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.182293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144302 restraints weight = 75621.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.149997 restraints weight = 36550.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153725 restraints weight = 21903.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156011 restraints weight = 15233.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157260 restraints weight = 12015.204| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15255 Z= 0.175 Angle : 0.607 25.186 20680 Z= 0.323 Chirality : 0.039 0.170 2275 Planarity : 0.005 0.039 2584 Dihedral : 10.101 80.138 2308 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -0.71 (0.19), residues: 1780 helix: 0.38 (0.18), residues: 799 sheet: -0.15 (0.36), residues: 194 loop : -1.43 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 116 TYR 0.018 0.002 TYR A 334 PHE 0.023 0.002 PHE A 520 TRP 0.010 0.002 TRP B 438 HIS 0.007 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00372 (15254) covalent geometry : angle 0.60670 (20678) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.39890 ( 2) hydrogen bonds : bond 0.04830 ( 733) hydrogen bonds : angle 4.75655 ( 2012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 299 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.667 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: A 12 MET cc_start: 0.6528 (ppp) cc_final: 0.6191 (ppp) REVERT: A 86 MET cc_start: 0.7755 (tpt) cc_final: 0.7156 (tpp) REVERT: A 155 MET cc_start: 0.5475 (tmm) cc_final: 0.4630 (tmm) REVERT: A 272 ASP cc_start: 0.7635 (m-30) cc_final: 0.7151 (t0) REVERT: A 561 MET cc_start: 0.5936 (tpp) cc_final: 0.5686 (tpp) REVERT: A 597 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6904 (mm-30) REVERT: A 656 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6390 (mm-30) REVERT: B 1 MET cc_start: 0.6982 (mpp) cc_final: 0.6675 (mpp) REVERT: B 88 VAL cc_start: 0.7060 (t) cc_final: 0.6682 (t) REVERT: B 218 LEU cc_start: 0.7920 (mt) cc_final: 0.7627 (tp) REVERT: B 277 GLU cc_start: 0.7842 (mp0) cc_final: 0.7551 (mm-30) REVERT: B 480 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6523 (mtmm) REVERT: B 507 MET cc_start: 0.8982 (mtp) cc_final: 0.8757 (mtp) REVERT: C 20 LEU cc_start: 0.8391 (mm) cc_final: 0.7875 (mm) REVERT: F 96 ASN cc_start: 0.8320 (t0) cc_final: 0.7159 (t0) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2528 time to fit residues: 110.7874 Evaluate side-chains 252 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 ASN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.179910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143619 restraints weight = 74464.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149042 restraints weight = 36917.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.152493 restraints weight = 22371.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.154467 restraints weight = 15754.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155963 restraints weight = 12576.285| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15255 Z= 0.162 Angle : 0.599 28.046 20680 Z= 0.315 Chirality : 0.039 0.170 2275 Planarity : 0.004 0.043 2584 Dihedral : 10.074 84.439 2308 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: -0.58 (0.19), residues: 1780 helix: 0.52 (0.18), residues: 802 sheet: -0.12 (0.38), residues: 189 loop : -1.40 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 454 TYR 0.017 0.002 TYR B 49 PHE 0.021 0.002 PHE A 520 TRP 0.029 0.002 TRP A 368 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00363 (15254) covalent geometry : angle 0.59894 (20678) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.46090 ( 2) hydrogen bonds : bond 0.04671 ( 733) hydrogen bonds : angle 4.70114 ( 2012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 294 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.715 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: A 86 MET cc_start: 0.7580 (tpt) cc_final: 0.7311 (tpp) REVERT: A 155 MET cc_start: 0.5497 (tmm) cc_final: 0.4678 (tmm) REVERT: A 272 ASP cc_start: 0.7498 (m-30) cc_final: 0.7208 (t0) REVERT: A 460 MET cc_start: 0.7580 (mmt) cc_final: 0.7336 (mmt) REVERT: A 597 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6725 (mm-30) REVERT: B 1 MET cc_start: 0.7399 (mpp) cc_final: 0.7089 (mpp) REVERT: B 135 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6908 (mtt90) REVERT: B 218 LEU cc_start: 0.7842 (mt) cc_final: 0.7561 (tp) REVERT: B 277 GLU cc_start: 0.7807 (mp0) cc_final: 0.7418 (mm-30) REVERT: B 480 LYS cc_start: 0.7053 (mmtm) cc_final: 0.6543 (mtmm) REVERT: C 11 MET cc_start: 0.6161 (ttm) cc_final: 0.5944 (mtp) REVERT: C 20 LEU cc_start: 0.8054 (mm) cc_final: 0.7425 (mm) REVERT: C 64 MET cc_start: 0.7489 (ttm) cc_final: 0.7265 (ttm) REVERT: F 18 LEU cc_start: 0.9034 (tt) cc_final: 0.8351 (tt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2574 time to fit residues: 110.8344 Evaluate side-chains 237 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 151 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 306 ASN B 425 ASN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.180558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.143974 restraints weight = 75149.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.149439 restraints weight = 37113.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152954 restraints weight = 22507.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154957 restraints weight = 15849.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156415 restraints weight = 12638.292| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15255 Z= 0.126 Angle : 0.571 26.876 20680 Z= 0.298 Chirality : 0.038 0.164 2275 Planarity : 0.004 0.046 2584 Dihedral : 10.046 86.281 2308 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -0.44 (0.19), residues: 1780 helix: 0.71 (0.18), residues: 803 sheet: -0.15 (0.38), residues: 187 loop : -1.37 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 45 TYR 0.013 0.001 TYR A 334 PHE 0.017 0.001 PHE B 730 TRP 0.025 0.002 TRP F 110 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00280 (15254) covalent geometry : angle 0.57120 (20678) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.32044 ( 2) hydrogen bonds : bond 0.04356 ( 733) hydrogen bonds : angle 4.52290 ( 2012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 283 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.598 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: A 86 MET cc_start: 0.7592 (tpt) cc_final: 0.7301 (tpp) REVERT: A 155 MET cc_start: 0.5493 (tmm) cc_final: 0.4599 (tmm) REVERT: A 204 ARG cc_start: 0.6612 (tmm-80) cc_final: 0.6204 (ttp80) REVERT: A 249 MET cc_start: 0.4977 (ttm) cc_final: 0.4382 (ttp) REVERT: A 272 ASP cc_start: 0.7539 (m-30) cc_final: 0.7288 (t0) REVERT: A 581 MET cc_start: 0.8235 (ttm) cc_final: 0.7728 (ttm) REVERT: A 597 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6669 (mm-30) REVERT: B 1 MET cc_start: 0.7396 (mpp) cc_final: 0.7103 (mpp) REVERT: B 3 VAL cc_start: 0.8362 (t) cc_final: 0.8109 (t) REVERT: B 135 ARG cc_start: 0.7047 (mtm-85) cc_final: 0.6838 (mtt90) REVERT: B 218 LEU cc_start: 0.7837 (mt) cc_final: 0.7526 (tp) REVERT: B 277 GLU cc_start: 0.7729 (mp0) cc_final: 0.7338 (mm-30) REVERT: B 356 MET cc_start: 0.7624 (tpt) cc_final: 0.7000 (tpt) REVERT: B 480 LYS cc_start: 0.6855 (mmtm) cc_final: 0.6382 (mtmm) REVERT: C 11 MET cc_start: 0.6185 (ttm) cc_final: 0.5780 (mtp) REVERT: C 20 LEU cc_start: 0.8347 (mm) cc_final: 0.7743 (mm) REVERT: C 206 MET cc_start: 0.8081 (tpp) cc_final: 0.7709 (tpp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2493 time to fit residues: 102.8669 Evaluate side-chains 225 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 170 optimal weight: 0.0470 chunk 146 optimal weight: 5.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 654 ASN C 73 GLN C 75 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.180016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143363 restraints weight = 75117.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.148780 restraints weight = 36741.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152252 restraints weight = 22175.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.154440 restraints weight = 15603.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155607 restraints weight = 12337.099| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15255 Z= 0.117 Angle : 0.561 27.049 20680 Z= 0.291 Chirality : 0.038 0.162 2275 Planarity : 0.004 0.059 2584 Dihedral : 10.059 88.133 2308 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -0.26 (0.20), residues: 1780 helix: 0.91 (0.19), residues: 803 sheet: -0.09 (0.38), residues: 186 loop : -1.32 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 350 TYR 0.013 0.001 TYR F 37 PHE 0.016 0.001 PHE B 730 TRP 0.021 0.001 TRP A 368 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00261 (15254) covalent geometry : angle 0.56094 (20678) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.50682 ( 2) hydrogen bonds : bond 0.04158 ( 733) hydrogen bonds : angle 4.41965 ( 2012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 282 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.819 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: A 86 MET cc_start: 0.7604 (tpt) cc_final: 0.7318 (tpp) REVERT: A 155 MET cc_start: 0.5479 (tmm) cc_final: 0.4519 (tmm) REVERT: A 249 MET cc_start: 0.4910 (ttm) cc_final: 0.4214 (ttp) REVERT: A 272 ASP cc_start: 0.7468 (m-30) cc_final: 0.7255 (t0) REVERT: A 318 LYS cc_start: 0.7530 (tppt) cc_final: 0.6834 (tttt) REVERT: A 581 MET cc_start: 0.8276 (ttm) cc_final: 0.7765 (ttm) REVERT: A 597 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6696 (mm-30) REVERT: A 656 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6533 (mm-30) REVERT: B 1 MET cc_start: 0.7377 (mpp) cc_final: 0.7155 (mpp) REVERT: B 3 VAL cc_start: 0.8402 (t) cc_final: 0.8169 (t) REVERT: B 96 GLU cc_start: 0.5899 (tm-30) cc_final: 0.5516 (tp30) REVERT: B 135 ARG cc_start: 0.6976 (mtm-85) cc_final: 0.6745 (mtt90) REVERT: B 218 LEU cc_start: 0.7791 (mt) cc_final: 0.7501 (tp) REVERT: B 225 ASN cc_start: 0.5383 (t0) cc_final: 0.5141 (t0) REVERT: B 260 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8245 (ttm-80) REVERT: B 277 GLU cc_start: 0.7754 (mp0) cc_final: 0.7305 (mm-30) REVERT: B 290 MET cc_start: 0.6346 (mmm) cc_final: 0.5945 (mmm) REVERT: B 356 MET cc_start: 0.7677 (tpt) cc_final: 0.7189 (tpt) REVERT: B 480 LYS cc_start: 0.6768 (mmtm) cc_final: 0.6363 (mtmm) REVERT: B 718 MET cc_start: 0.8387 (mtp) cc_final: 0.8102 (mtp) REVERT: C 20 LEU cc_start: 0.8091 (mm) cc_final: 0.7340 (mm) REVERT: C 64 MET cc_start: 0.7467 (ttm) cc_final: 0.7231 (ttm) REVERT: C 82 ASN cc_start: 0.7058 (m-40) cc_final: 0.6504 (m-40) REVERT: C 87 ASP cc_start: 0.6826 (p0) cc_final: 0.6466 (p0) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2913 time to fit residues: 120.5211 Evaluate side-chains 233 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 117 optimal weight: 0.0370 chunk 6 optimal weight: 20.0000 chunk 162 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 73 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.178968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142012 restraints weight = 75246.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147342 restraints weight = 37570.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150847 restraints weight = 22936.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152797 restraints weight = 16181.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154300 restraints weight = 12985.101| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15255 Z= 0.126 Angle : 0.560 26.673 20680 Z= 0.290 Chirality : 0.038 0.155 2275 Planarity : 0.004 0.045 2584 Dihedral : 10.041 90.215 2308 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.16 (0.20), residues: 1780 helix: 1.01 (0.19), residues: 798 sheet: 0.04 (0.39), residues: 184 loop : -1.31 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.019 0.001 TYR A 564 PHE 0.016 0.001 PHE B 730 TRP 0.021 0.001 TRP A 368 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00281 (15254) covalent geometry : angle 0.56018 (20678) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.46404 ( 2) hydrogen bonds : bond 0.04182 ( 733) hydrogen bonds : angle 4.40463 ( 2012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 284 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.687 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: A 86 MET cc_start: 0.7594 (tpt) cc_final: 0.7266 (tpp) REVERT: A 155 MET cc_start: 0.5477 (tmm) cc_final: 0.4521 (tmm) REVERT: A 249 MET cc_start: 0.4914 (ttm) cc_final: 0.4245 (ttp) REVERT: A 318 LYS cc_start: 0.7609 (tppt) cc_final: 0.6929 (tttt) REVERT: A 581 MET cc_start: 0.8262 (ttm) cc_final: 0.7739 (ttm) REVERT: A 597 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6785 (mm-30) REVERT: B 1 MET cc_start: 0.7380 (mpp) cc_final: 0.7154 (mpp) REVERT: B 3 VAL cc_start: 0.8530 (t) cc_final: 0.8306 (t) REVERT: B 96 GLU cc_start: 0.6087 (tm-30) cc_final: 0.5716 (tp30) REVERT: B 135 ARG cc_start: 0.7004 (mtm-85) cc_final: 0.6775 (mtt90) REVERT: B 218 LEU cc_start: 0.7909 (mt) cc_final: 0.7624 (tp) REVERT: B 277 GLU cc_start: 0.7777 (mp0) cc_final: 0.7332 (mm-30) REVERT: B 309 TRP cc_start: 0.8546 (t-100) cc_final: 0.8113 (t-100) REVERT: B 347 LYS cc_start: 0.8749 (ptpp) cc_final: 0.8331 (ptpp) REVERT: B 356 MET cc_start: 0.7680 (tpt) cc_final: 0.7219 (tpt) REVERT: B 480 LYS cc_start: 0.6783 (mmtm) cc_final: 0.6397 (mtmm) REVERT: C 20 LEU cc_start: 0.8243 (mm) cc_final: 0.7817 (mm) REVERT: C 64 MET cc_start: 0.7368 (ttm) cc_final: 0.7154 (ttm) REVERT: C 82 ASN cc_start: 0.6960 (m-40) cc_final: 0.6354 (m-40) REVERT: C 87 ASP cc_start: 0.6838 (p0) cc_final: 0.6497 (p0) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2630 time to fit residues: 109.5030 Evaluate side-chains 229 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.0070 chunk 131 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.180552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143913 restraints weight = 75484.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.149329 restraints weight = 37300.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152833 restraints weight = 22648.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.155007 restraints weight = 15987.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156117 restraints weight = 12684.005| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15255 Z= 0.102 Angle : 0.547 26.717 20680 Z= 0.280 Chirality : 0.037 0.152 2275 Planarity : 0.004 0.048 2584 Dihedral : 9.964 91.444 2308 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.20), residues: 1780 helix: 1.20 (0.19), residues: 799 sheet: 0.09 (0.40), residues: 183 loop : -1.22 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 498 TYR 0.012 0.001 TYR B 497 PHE 0.014 0.001 PHE B 730 TRP 0.019 0.001 TRP A 368 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00224 (15254) covalent geometry : angle 0.54662 (20678) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.31510 ( 2) hydrogen bonds : bond 0.03821 ( 733) hydrogen bonds : angle 4.21233 ( 2012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 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 279 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.805 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: A 86 MET cc_start: 0.7715 (tpt) cc_final: 0.7251 (tpp) REVERT: A 155 MET cc_start: 0.5424 (tmm) cc_final: 0.4452 (tmm) REVERT: A 249 MET cc_start: 0.4779 (ttm) cc_final: 0.4093 (ttp) REVERT: A 318 LYS cc_start: 0.7543 (tppt) cc_final: 0.6937 (tttt) REVERT: A 581 MET cc_start: 0.8216 (ttm) cc_final: 0.7668 (ttm) REVERT: A 597 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6716 (mm-30) REVERT: B 3 VAL cc_start: 0.8493 (t) cc_final: 0.8264 (t) REVERT: B 96 GLU cc_start: 0.5978 (tm-30) cc_final: 0.5608 (tp30) REVERT: B 135 ARG cc_start: 0.6974 (mtm-85) cc_final: 0.6768 (mtt90) REVERT: B 218 LEU cc_start: 0.7839 (mt) cc_final: 0.7577 (tp) REVERT: B 277 GLU cc_start: 0.7684 (mp0) cc_final: 0.7288 (mm-30) REVERT: B 290 MET cc_start: 0.6231 (mmm) cc_final: 0.5907 (mmm) REVERT: B 309 TRP cc_start: 0.8287 (t-100) cc_final: 0.8044 (t-100) REVERT: B 347 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8262 (ptpp) REVERT: B 356 MET cc_start: 0.7618 (tpt) cc_final: 0.7185 (tpt) REVERT: B 409 MET cc_start: 0.4189 (tmm) cc_final: 0.3963 (tmm) REVERT: B 480 LYS cc_start: 0.6621 (mmtm) cc_final: 0.6198 (mtmm) REVERT: C 20 LEU cc_start: 0.8108 (mm) cc_final: 0.7292 (mm) REVERT: C 64 MET cc_start: 0.7424 (ttm) cc_final: 0.7157 (ttm) REVERT: C 82 ASN cc_start: 0.7100 (m-40) cc_final: 0.6441 (m-40) REVERT: C 87 ASP cc_start: 0.6895 (p0) cc_final: 0.6537 (p0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3063 time to fit residues: 124.2993 Evaluate side-chains 231 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 168 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN C 73 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.178961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141495 restraints weight = 76475.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.147059 restraints weight = 37011.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150702 restraints weight = 22277.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152957 restraints weight = 15578.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.154149 restraints weight = 12295.673| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.7940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 15255 Z= 0.120 Angle : 0.549 26.585 20680 Z= 0.284 Chirality : 0.038 0.165 2275 Planarity : 0.004 0.044 2584 Dihedral : 9.973 92.891 2308 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.20), residues: 1780 helix: 1.23 (0.19), residues: 791 sheet: 0.07 (0.40), residues: 183 loop : -1.20 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 498 TYR 0.009 0.001 TYR B 217 PHE 0.014 0.001 PHE B 730 TRP 0.020 0.001 TRP A 368 HIS 0.004 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00275 (15254) covalent geometry : angle 0.54913 (20678) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.45341 ( 2) hydrogen bonds : bond 0.04011 ( 733) hydrogen bonds : angle 4.26825 ( 2012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4872.90 seconds wall clock time: 83 minutes 48.19 seconds (5028.19 seconds total)