Starting phenix.real_space_refine on Mon Aug 25 15:19:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nj5_12373/08_2025/7nj5_12373.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj5_12373/08_2025/7nj5_12373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nj5_12373/08_2025/7nj5_12373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj5_12373/08_2025/7nj5_12373.map" model { file = "/net/cci-nas-00/data/ceres_data/7nj5_12373/08_2025/7nj5_12373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj5_12373/08_2025/7nj5_12373.cif" } resolution = 4.63 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= 0.032 sd= 0.275 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 9327 2.51 5 N 2602 2.21 5 O 2880 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: 28806 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: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 96} Chain breaks: 3 Time building chain proxies: 4.52, per 1000 atoms: 0.16 Number of scatterers: 28806 At special positions: 0 Unit cell: (102, 110, 162, 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 2880 8.00 N 2602 7.00 C 9327 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.38 Conformation dependent library (CDL) restraints added in 637.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.4% alpha, 15.5% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.141A 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: 5.020A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A 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: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A 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: 4.635A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.733A 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: 3.530A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.826A 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: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A 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: 3.978A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.658A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.619A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A 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: 3.836A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A 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: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A 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: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.516A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.635A 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: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.974A 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 4 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.161A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER F 124 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL F 12 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL F 121 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL F 93 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 33 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.161A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER F 124 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL F 12 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL F 121 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL F 93 " --> pdb=" O VAL F 121 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 1995 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: 6.65 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13841 1.04 - 1.23: 646 1.23 - 1.43: 5875 1.43 - 1.63: 8610 1.63 - 1.83: 183 Bond restraints: 29155 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.522 -0.064 1.40e-02 5.10e+03 2.12e+01 bond pdb=" CE1 HIS F 59 " pdb=" NE2 HIS F 59 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.21e+01 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.40e-02 5.10e+03 9.96e+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 6.44e+00 ... (remaining 29150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52287 5.65 - 11.30: 19 11.30 - 16.94: 0 16.94 - 22.59: 1 22.59 - 28.24: 5 Bond angle restraints: 52312 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 79.76 28.24 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 80.35 27.65 3.00e+00 1.11e-01 8.50e+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 81.83 27.17 3.00e+00 1.11e-01 8.20e+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 82.45 26.55 3.00e+00 1.11e-01 7.83e+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 7.05e+01 ... (remaining 52307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12573 17.93 - 35.85: 859 35.85 - 53.78: 253 53.78 - 71.71: 89 71.71 - 89.63: 17 Dihedral angle restraints: 13791 sinusoidal: 7729 harmonic: 6062 Sorted by residual: dihedral pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual 122.80 137.99 -15.19 0 2.50e+00 1.60e-01 3.69e+01 dihedral pdb=" C SER F 85 " pdb=" N SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 13788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2205 0.112 - 0.225: 58 0.225 - 0.337: 4 0.337 - 0.450: 2 0.450 - 0.562: 1 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CA SER F 85 " pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CB SER F 85 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA ASN F 77 " pdb=" N ASN F 77 " pdb=" C ASN F 77 " pdb=" CB ASN F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA LYS F 65 " pdb=" N LYS F 65 " pdb=" C LYS F 65 " pdb=" CB LYS F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 2267 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 94 " -0.017 2.00e-02 2.50e+03 4.95e-02 4.90e+01 pdb=" CG TYR F 94 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 94 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 94 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR F 94 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR F 94 " 0.062 2.00e-02 2.50e+03 pdb=" OH TYR F 94 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " 0.017 2.00e-02 2.50e+03 4.83e-02 4.67e+01 pdb=" CG TYR F 32 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 115 " 0.070 2.00e-02 2.50e+03 3.40e-02 2.89e+01 pdb=" CG TRP F 115 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP F 115 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP F 115 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP F 115 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP F 115 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 115 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 115 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 115 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP F 115 " 0.031 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1262 2.17 - 2.78: 56261 2.78 - 3.39: 80851 3.39 - 3.99: 105858 3.99 - 4.60: 165202 Nonbonded interactions: 409434 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 1.569 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.602 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409429 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5144 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 0.064 15287 Z= 0.245 Angle : 0.731 26.860 20719 Z= 0.431 Chirality : 0.046 0.562 2270 Planarity : 0.005 0.090 2589 Dihedral : 14.354 89.632 5973 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.32 % Allowed : 0.25 % Favored : 99.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 1784 helix: 0.45 (0.19), residues: 786 sheet: -0.71 (0.36), residues: 183 loop : -1.31 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG F 72 TYR 0.094 0.003 TYR F 94 PHE 0.048 0.002 PHE A 446 TRP 0.070 0.002 TRP F 115 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00438 (15287) covalent geometry : angle 0.73068 (20719) hydrogen bonds : bond 0.15249 ( 732) hydrogen bonds : angle 6.05058 ( 2015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 407 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 402 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 ILE cc_start: 0.8127 (mt) cc_final: 0.7822 (tp) REVERT: A 522 SER cc_start: 0.8326 (m) cc_final: 0.8108 (t) REVERT: A 528 THR cc_start: 0.7469 (m) cc_final: 0.7147 (p) REVERT: A 540 TYR cc_start: 0.7099 (m-80) cc_final: 0.6881 (m-80) REVERT: A 633 ILE cc_start: 0.6114 (tt) cc_final: 0.5735 (tp) REVERT: A 648 SER cc_start: 0.9094 (t) cc_final: 0.8487 (m) REVERT: B 40 MET cc_start: 0.8049 (mtm) cc_final: 0.7275 (ttm) REVERT: B 229 LYS cc_start: 0.8336 (tttp) cc_final: 0.8134 (ttmm) REVERT: B 407 MET cc_start: 0.6422 (mmm) cc_final: 0.5916 (tpp) REVERT: B 446 ASP cc_start: 0.9092 (m-30) cc_final: 0.8690 (m-30) REVERT: B 509 LEU cc_start: 0.9586 (tp) cc_final: 0.9382 (tp) REVERT: B 561 CYS cc_start: 0.5949 (p) cc_final: 0.5123 (p) REVERT: B 568 ILE cc_start: 0.8315 (mt) cc_final: 0.7776 (tt) REVERT: B 612 LYS cc_start: 0.7594 (mttt) cc_final: 0.6572 (mttt) REVERT: C 42 ASN cc_start: 0.8592 (t0) cc_final: 0.7403 (p0) REVERT: F 12 VAL cc_start: -0.2206 (OUTLIER) cc_final: -0.2686 (m) outliers start: 5 outliers final: 1 residues processed: 406 average time/residue: 0.2743 time to fit residues: 159.2332 Evaluate side-chains 261 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.135265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.114314 restraints weight = 161330.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.119802 restraints weight = 82201.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.123456 restraints weight = 48168.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.125839 restraints weight = 31174.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.127436 restraints weight = 22083.392| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15287 Z= 0.160 Angle : 0.597 27.438 20719 Z= 0.318 Chirality : 0.039 0.166 2270 Planarity : 0.005 0.055 2589 Dihedral : 10.128 73.353 2314 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 1784 helix: 0.41 (0.18), residues: 781 sheet: -0.56 (0.37), residues: 192 loop : -1.21 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 72 TYR 0.014 0.001 TYR A 393 PHE 0.025 0.002 PHE A 446 TRP 0.010 0.001 TRP A 422 HIS 0.010 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00325 (15287) covalent geometry : angle 0.59728 (20719) hydrogen bonds : bond 0.04759 ( 732) hydrogen bonds : angle 5.08558 ( 2015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 THR cc_start: 0.7824 (p) cc_final: 0.7622 (p) REVERT: A 334 TYR cc_start: 0.7747 (m-80) cc_final: 0.6892 (m-80) REVERT: A 477 MET cc_start: 0.8803 (pmm) cc_final: 0.8478 (mtt) REVERT: A 483 ILE cc_start: 0.8870 (mt) cc_final: 0.8511 (tp) REVERT: A 528 THR cc_start: 0.7874 (m) cc_final: 0.7478 (p) REVERT: A 579 MET cc_start: 0.7958 (tmm) cc_final: 0.7447 (tmm) REVERT: A 633 ILE cc_start: 0.6127 (tt) cc_final: 0.5675 (tp) REVERT: A 648 SER cc_start: 0.9106 (t) cc_final: 0.8336 (m) REVERT: B 3 VAL cc_start: 0.6792 (t) cc_final: 0.6223 (t) REVERT: B 229 LYS cc_start: 0.8681 (tttp) cc_final: 0.8450 (ttmm) REVERT: B 407 MET cc_start: 0.6707 (mmm) cc_final: 0.6018 (tpp) REVERT: B 494 SER cc_start: 0.8037 (p) cc_final: 0.7315 (p) REVERT: B 509 LEU cc_start: 0.9516 (tp) cc_final: 0.9231 (mt) REVERT: B 561 CYS cc_start: 0.6343 (p) cc_final: 0.5487 (p) REVERT: B 568 ILE cc_start: 0.8633 (mt) cc_final: 0.8121 (tt) REVERT: B 656 GLU cc_start: 0.8826 (tt0) cc_final: 0.8519 (tt0) REVERT: B 685 ASP cc_start: 0.7772 (t0) cc_final: 0.7551 (t70) REVERT: B 718 MET cc_start: 0.8515 (mtm) cc_final: 0.7299 (mmm) REVERT: C 23 THR cc_start: 0.8698 (m) cc_final: 0.8253 (p) REVERT: C 42 ASN cc_start: 0.8651 (t0) cc_final: 0.7395 (p0) REVERT: C 66 MET cc_start: 0.6408 (mmp) cc_final: 0.6191 (mmm) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2401 time to fit residues: 103.8287 Evaluate side-chains 238 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 19 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 169 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN B 65 GLN B 292 ASN B 313 GLN B 582 GLN B 605 HIS ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 182 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 = 0.4234 r_free = 0.4234 target = 0.120251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.098731 restraints weight = 173136.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.103518 restraints weight = 89512.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106669 restraints weight = 53984.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.108832 restraints weight = 36691.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.110256 restraints weight = 27244.858| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.196 15287 Z= 0.301 Angle : 0.770 25.766 20719 Z= 0.420 Chirality : 0.042 0.213 2270 Planarity : 0.008 0.189 2589 Dihedral : 10.441 73.738 2314 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 0.19 % Allowed : 2.52 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.18), residues: 1784 helix: -0.52 (0.17), residues: 799 sheet: -0.76 (0.35), residues: 197 loop : -1.56 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.001 ARG C 142 TYR 0.024 0.003 TYR B 355 PHE 0.043 0.003 PHE B 412 TRP 0.035 0.003 TRP C 99 HIS 0.017 0.003 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00649 (15287) covalent geometry : angle 0.76988 (20719) hydrogen bonds : bond 0.05050 ( 732) hydrogen bonds : angle 5.54233 ( 2015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 261 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.8740 (m-80) cc_final: 0.7933 (m-80) REVERT: A 477 MET cc_start: 0.8902 (pmm) cc_final: 0.8582 (mpp) REVERT: A 579 MET cc_start: 0.8365 (tmm) cc_final: 0.7210 (tmm) REVERT: B 229 LYS cc_start: 0.8716 (tttp) cc_final: 0.8228 (ttpt) REVERT: B 284 ASN cc_start: 0.8191 (m-40) cc_final: 0.7969 (m-40) REVERT: B 407 MET cc_start: 0.8539 (mmm) cc_final: 0.7802 (mmt) REVERT: B 507 MET cc_start: 0.8003 (mmm) cc_final: 0.7603 (mmm) REVERT: B 559 TYR cc_start: 0.7708 (m-80) cc_final: 0.7140 (m-10) REVERT: B 568 ILE cc_start: 0.8982 (mt) cc_final: 0.8092 (tp) REVERT: B 620 TYR cc_start: 0.6265 (t80) cc_final: 0.5721 (t80) REVERT: B 649 HIS cc_start: 0.7219 (t-90) cc_final: 0.6892 (t-90) REVERT: B 656 GLU cc_start: 0.8846 (tt0) cc_final: 0.8596 (tt0) REVERT: B 690 GLN cc_start: 0.8256 (mm-40) cc_final: 0.8041 (tm-30) REVERT: C 7 LEU cc_start: 0.8248 (tt) cc_final: 0.7978 (tt) REVERT: C 23 THR cc_start: 0.8985 (m) cc_final: 0.8710 (p) REVERT: F 34 MET cc_start: -0.0368 (mpp) cc_final: -0.0687 (mmt) REVERT: F 83 MET cc_start: 0.8398 (mpp) cc_final: 0.7956 (mpp) outliers start: 3 outliers final: 1 residues processed: 261 average time/residue: 0.2377 time to fit residues: 94.6548 Evaluate side-chains 211 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 80 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 99 optimal weight: 0.0270 chunk 7 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 664 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.120479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.099077 restraints weight = 173375.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.103848 restraints weight = 88880.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.107017 restraints weight = 53410.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.109127 restraints weight = 36345.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.110410 restraints weight = 27262.101| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15287 Z= 0.150 Angle : 0.582 27.722 20719 Z= 0.310 Chirality : 0.038 0.166 2270 Planarity : 0.005 0.099 2589 Dihedral : 10.199 73.562 2314 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.19), residues: 1784 helix: 0.14 (0.18), residues: 788 sheet: -0.64 (0.35), residues: 205 loop : -1.45 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 125 TYR 0.020 0.002 TYR A 130 PHE 0.022 0.002 PHE B 730 TRP 0.012 0.002 TRP C 99 HIS 0.009 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00318 (15287) covalent geometry : angle 0.58188 (20719) hydrogen bonds : bond 0.04136 ( 732) hydrogen bonds : angle 5.02257 ( 2015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 257 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.8894 (mmp) cc_final: 0.8689 (mmm) REVERT: A 214 LEU cc_start: 0.8215 (mt) cc_final: 0.7937 (mt) REVERT: A 334 TYR cc_start: 0.8813 (m-80) cc_final: 0.8045 (m-80) REVERT: A 360 MET cc_start: 0.8045 (mtm) cc_final: 0.7608 (mpp) REVERT: A 477 MET cc_start: 0.8809 (pmm) cc_final: 0.8559 (mtp) REVERT: A 579 MET cc_start: 0.7926 (tmm) cc_final: 0.7393 (tmm) REVERT: B 229 LYS cc_start: 0.8728 (tttp) cc_final: 0.7979 (tppp) REVERT: B 407 MET cc_start: 0.8378 (mmm) cc_final: 0.7670 (mmt) REVERT: B 507 MET cc_start: 0.7735 (mmm) cc_final: 0.7389 (mmm) REVERT: B 559 TYR cc_start: 0.7255 (m-80) cc_final: 0.6965 (m-10) REVERT: B 649 HIS cc_start: 0.6962 (t-90) cc_final: 0.6761 (t70) REVERT: B 690 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8022 (tm-30) REVERT: B 718 MET cc_start: 0.8870 (mtp) cc_final: 0.8624 (mtp) REVERT: C 23 THR cc_start: 0.9005 (m) cc_final: 0.8740 (p) REVERT: F 94 TYR cc_start: 0.8565 (m-80) cc_final: 0.8333 (m-80) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2178 time to fit residues: 86.8405 Evaluate side-chains 210 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 101 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 145 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 456 HIS B 641 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.116534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.094615 restraints weight = 173946.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.099333 restraints weight = 87693.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.102527 restraints weight = 52673.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.104691 restraints weight = 35726.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.106122 restraints weight = 26694.361| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15287 Z= 0.177 Angle : 0.603 26.719 20719 Z= 0.320 Chirality : 0.039 0.183 2270 Planarity : 0.005 0.072 2589 Dihedral : 10.243 74.058 2314 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.83 (0.19), residues: 1784 helix: 0.42 (0.18), residues: 782 sheet: -0.47 (0.38), residues: 187 loop : -1.52 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 125 TYR 0.019 0.002 TYR A 110 PHE 0.024 0.002 PHE B 730 TRP 0.019 0.002 TRP C 99 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00372 (15287) covalent geometry : angle 0.60256 (20719) hydrogen bonds : bond 0.04041 ( 732) hydrogen bonds : angle 4.98597 ( 2015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 THR cc_start: 0.8266 (p) cc_final: 0.8055 (p) REVERT: A 211 MET cc_start: 0.5046 (ttt) cc_final: 0.4522 (ttt) REVERT: A 214 LEU cc_start: 0.8463 (mt) cc_final: 0.8170 (mt) REVERT: A 276 CYS cc_start: 0.7777 (m) cc_final: 0.7538 (m) REVERT: A 334 TYR cc_start: 0.8786 (m-80) cc_final: 0.8265 (m-80) REVERT: B 319 LEU cc_start: 0.9416 (tt) cc_final: 0.9192 (tp) REVERT: B 407 MET cc_start: 0.8335 (mmm) cc_final: 0.6745 (tpp) REVERT: B 649 HIS cc_start: 0.7279 (t-90) cc_final: 0.7004 (t-90) REVERT: B 690 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8080 (tm-30) REVERT: B 718 MET cc_start: 0.9003 (mtp) cc_final: 0.8729 (mtp) REVERT: C 23 THR cc_start: 0.9087 (m) cc_final: 0.8846 (p) REVERT: C 50 MET cc_start: 0.8018 (tpp) cc_final: 0.7752 (tpp) REVERT: C 90 MET cc_start: 0.6379 (ptp) cc_final: 0.6156 (ptp) REVERT: F 83 MET cc_start: 0.8357 (mpp) cc_final: 0.7955 (mpp) REVERT: F 94 TYR cc_start: 0.8404 (m-80) cc_final: 0.8179 (m-80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2196 time to fit residues: 81.2140 Evaluate side-chains 205 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 39 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.108900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.087593 restraints weight = 185370.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.091806 restraints weight = 96275.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.094689 restraints weight = 59196.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.096650 restraints weight = 41067.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.097781 restraints weight = 31208.556| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15287 Z= 0.251 Angle : 0.699 27.592 20719 Z= 0.380 Chirality : 0.041 0.184 2270 Planarity : 0.006 0.090 2589 Dihedral : 10.580 78.574 2314 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.18), residues: 1784 helix: -0.15 (0.17), residues: 797 sheet: -0.77 (0.36), residues: 198 loop : -1.73 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 716 TYR 0.034 0.002 TYR B 82 PHE 0.032 0.003 PHE B 150 TRP 0.019 0.003 TRP A 368 HIS 0.011 0.002 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00515 (15287) covalent geometry : angle 0.69892 (20719) hydrogen bonds : bond 0.04561 ( 732) hydrogen bonds : angle 5.35112 ( 2015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 230 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.9045 (mmp) cc_final: 0.8784 (mmm) REVERT: A 211 MET cc_start: 0.6881 (ttt) cc_final: 0.6664 (ttm) REVERT: A 276 CYS cc_start: 0.8271 (m) cc_final: 0.8019 (m) REVERT: A 285 MET cc_start: 0.8313 (tmm) cc_final: 0.8046 (tmm) REVERT: A 344 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 485 MET cc_start: 0.7420 (mtm) cc_final: 0.7217 (mtt) REVERT: B 491 GLU cc_start: 0.7602 (mp0) cc_final: 0.7269 (mp0) REVERT: B 507 MET cc_start: 0.7925 (mmm) cc_final: 0.7431 (mmm) REVERT: B 690 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8298 (tm-30) REVERT: B 718 MET cc_start: 0.9243 (mtp) cc_final: 0.8842 (mtp) REVERT: C 164 MET cc_start: 0.9056 (mtt) cc_final: 0.8426 (ttt) REVERT: F 83 MET cc_start: 0.8399 (mpp) cc_final: 0.8001 (mpp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2147 time to fit residues: 75.6466 Evaluate side-chains 191 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 113 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 67 optimal weight: 0.0770 chunk 141 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.108039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086908 restraints weight = 184407.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.091290 restraints weight = 93865.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.094169 restraints weight = 56494.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.096161 restraints weight = 38832.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.097533 restraints weight = 29264.024| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15287 Z= 0.167 Angle : 0.599 25.870 20719 Z= 0.320 Chirality : 0.039 0.213 2270 Planarity : 0.005 0.057 2589 Dihedral : 10.525 80.959 2314 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 1784 helix: 0.20 (0.18), residues: 806 sheet: -0.78 (0.36), residues: 200 loop : -1.76 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 663 TYR 0.025 0.002 TYR B 82 PHE 0.024 0.002 PHE B 730 TRP 0.013 0.002 TRP A 368 HIS 0.008 0.002 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00342 (15287) covalent geometry : angle 0.59891 (20719) hydrogen bonds : bond 0.04151 ( 732) hydrogen bonds : angle 5.02812 ( 2015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 231 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 MET cc_start: 0.8008 (tmm) cc_final: 0.7680 (tmm) REVERT: A 344 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7239 (mm-30) REVERT: A 485 MET cc_start: 0.7400 (mtm) cc_final: 0.6932 (mtt) REVERT: B 507 MET cc_start: 0.7732 (mmm) cc_final: 0.7415 (mmm) REVERT: B 645 MET cc_start: 0.8099 (mpp) cc_final: 0.7589 (mpp) REVERT: B 646 MET cc_start: 0.7094 (tpt) cc_final: 0.6413 (ppp) REVERT: B 690 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8366 (tm-30) REVERT: B 718 MET cc_start: 0.9314 (mtp) cc_final: 0.8918 (mtp) REVERT: C 42 ASN cc_start: 0.8756 (t0) cc_final: 0.8179 (t0) REVERT: C 161 ASP cc_start: 0.8774 (m-30) cc_final: 0.8551 (m-30) REVERT: C 208 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8907 (tm-30) REVERT: F 83 MET cc_start: 0.8211 (mpp) cc_final: 0.7798 (mpp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2419 time to fit residues: 84.4837 Evaluate side-chains 192 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 75 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.107488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.086398 restraints weight = 186116.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.090717 restraints weight = 94502.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.093613 restraints weight = 57410.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.095575 restraints weight = 39439.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.096879 restraints weight = 29924.113| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15287 Z= 0.150 Angle : 0.583 27.833 20719 Z= 0.308 Chirality : 0.038 0.188 2270 Planarity : 0.004 0.059 2589 Dihedral : 10.491 82.544 2314 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1784 helix: 0.32 (0.18), residues: 815 sheet: -0.78 (0.37), residues: 200 loop : -1.78 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 116 TYR 0.019 0.002 TYR B 82 PHE 0.030 0.002 PHE A 315 TRP 0.011 0.002 TRP A 317 HIS 0.007 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00315 (15287) covalent geometry : angle 0.58291 (20719) hydrogen bonds : bond 0.03940 ( 732) hydrogen bonds : angle 4.86176 ( 2015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 227 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 CYS cc_start: 0.8057 (m) cc_final: 0.7750 (m) REVERT: A 285 MET cc_start: 0.8006 (tmm) cc_final: 0.7641 (tmm) REVERT: A 344 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7662 (mt-10) REVERT: A 597 GLU cc_start: 0.8598 (pt0) cc_final: 0.8321 (pp20) REVERT: A 681 PHE cc_start: 0.5326 (m-10) cc_final: 0.4827 (m-80) REVERT: B 279 LYS cc_start: 0.7804 (mttt) cc_final: 0.7062 (pttp) REVERT: B 507 MET cc_start: 0.7726 (mmm) cc_final: 0.7462 (mmm) REVERT: B 555 TYR cc_start: 0.8720 (t80) cc_final: 0.7350 (t80) REVERT: B 646 MET cc_start: 0.7036 (tpt) cc_final: 0.6368 (ppp) REVERT: B 716 GLU cc_start: 0.7712 (mp0) cc_final: 0.7368 (tp30) REVERT: B 718 MET cc_start: 0.9385 (mtp) cc_final: 0.8911 (mtp) REVERT: C 7 LEU cc_start: 0.8989 (tt) cc_final: 0.8668 (tt) REVERT: C 42 ASN cc_start: 0.8836 (t0) cc_final: 0.8179 (t0) REVERT: C 161 ASP cc_start: 0.8799 (m-30) cc_final: 0.8586 (m-30) REVERT: F 34 MET cc_start: 0.1000 (mpp) cc_final: 0.0217 (mmt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2324 time to fit residues: 79.9124 Evaluate side-chains 194 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 6 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.108438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087530 restraints weight = 182175.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.091916 restraints weight = 91511.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.094890 restraints weight = 55069.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.096854 restraints weight = 37561.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.098248 restraints weight = 28281.984| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.8057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15287 Z= 0.113 Angle : 0.554 26.972 20719 Z= 0.290 Chirality : 0.038 0.162 2270 Planarity : 0.004 0.051 2589 Dihedral : 10.409 84.250 2314 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.77 (0.19), residues: 1784 helix: 0.62 (0.18), residues: 814 sheet: -0.56 (0.39), residues: 186 loop : -1.72 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.017 0.001 TYR A 334 PHE 0.021 0.001 PHE B 730 TRP 0.010 0.001 TRP A 406 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00247 (15287) covalent geometry : angle 0.55415 (20719) hydrogen bonds : bond 0.03760 ( 732) hydrogen bonds : angle 4.68768 ( 2015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8858 (mt) cc_final: 0.8585 (mt) REVERT: A 285 MET cc_start: 0.7927 (tmm) cc_final: 0.7571 (tmm) REVERT: A 597 GLU cc_start: 0.8556 (pt0) cc_final: 0.8273 (pp20) REVERT: A 681 PHE cc_start: 0.4835 (m-10) cc_final: 0.4120 (m-80) REVERT: B 507 MET cc_start: 0.7500 (mmm) cc_final: 0.7170 (mmm) REVERT: B 551 PHE cc_start: 0.8371 (t80) cc_final: 0.8148 (t80) REVERT: B 646 MET cc_start: 0.6979 (tpt) cc_final: 0.6325 (ppp) REVERT: B 690 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8632 (tp40) REVERT: B 718 MET cc_start: 0.9348 (mtp) cc_final: 0.8890 (mtp) REVERT: C 7 LEU cc_start: 0.9002 (tt) cc_final: 0.8697 (tt) REVERT: C 42 ASN cc_start: 0.8812 (t0) cc_final: 0.8165 (t0) REVERT: C 90 MET cc_start: 0.7036 (ptp) cc_final: 0.6294 (ptp) REVERT: C 164 MET cc_start: 0.8959 (mtt) cc_final: 0.8363 (ttt) REVERT: C 202 MET cc_start: 0.8837 (mmm) cc_final: 0.8191 (mmp) REVERT: F 34 MET cc_start: 0.0839 (mpp) cc_final: 0.0145 (mmt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2353 time to fit residues: 81.0225 Evaluate side-chains 190 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 70 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.107200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.086419 restraints weight = 184615.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.090700 restraints weight = 93514.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093572 restraints weight = 56711.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.095512 restraints weight = 38931.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.096785 restraints weight = 29502.327| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.8320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15287 Z= 0.131 Angle : 0.567 27.158 20719 Z= 0.297 Chirality : 0.038 0.189 2270 Planarity : 0.004 0.052 2589 Dihedral : 10.423 85.976 2314 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.75 (0.19), residues: 1784 helix: 0.64 (0.18), residues: 813 sheet: -0.69 (0.37), residues: 201 loop : -1.70 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.013 0.001 TYR B 82 PHE 0.020 0.001 PHE B 730 TRP 0.012 0.001 TRP A 406 HIS 0.007 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00276 (15287) covalent geometry : angle 0.56732 (20719) hydrogen bonds : bond 0.03759 ( 732) hydrogen bonds : angle 4.73056 ( 2015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 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 226 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8878 (t0) cc_final: 0.8487 (m110) REVERT: A 344 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 575 MET cc_start: 0.8314 (mtm) cc_final: 0.8093 (mtm) REVERT: A 597 GLU cc_start: 0.8849 (pt0) cc_final: 0.8395 (pp20) REVERT: A 681 PHE cc_start: 0.5076 (m-10) cc_final: 0.4252 (m-80) REVERT: B 179 MET cc_start: 0.6384 (mtm) cc_final: 0.5704 (mtp) REVERT: B 279 LYS cc_start: 0.7832 (mttt) cc_final: 0.7111 (pptt) REVERT: B 407 MET cc_start: 0.8250 (mmm) cc_final: 0.7257 (tpp) REVERT: B 507 MET cc_start: 0.7514 (mmm) cc_final: 0.7163 (mmm) REVERT: B 546 MET cc_start: 0.8794 (mmm) cc_final: 0.8504 (mmm) REVERT: B 551 PHE cc_start: 0.8622 (t80) cc_final: 0.8369 (t80) REVERT: B 646 MET cc_start: 0.6946 (tpt) cc_final: 0.6271 (ppp) REVERT: B 718 MET cc_start: 0.9379 (mtp) cc_final: 0.8928 (mtp) REVERT: C 7 LEU cc_start: 0.9020 (tt) cc_final: 0.8686 (tt) REVERT: C 42 ASN cc_start: 0.8809 (t0) cc_final: 0.8147 (t0) REVERT: C 90 MET cc_start: 0.7134 (ptp) cc_final: 0.6355 (ptp) REVERT: C 164 MET cc_start: 0.8935 (mtt) cc_final: 0.8369 (ttt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2615 time to fit residues: 89.5503 Evaluate side-chains 195 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 81 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.105205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.084382 restraints weight = 187807.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.088565 restraints weight = 95162.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.091372 restraints weight = 57834.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.093332 restraints weight = 39959.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.094480 restraints weight = 30246.420| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.8737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15287 Z= 0.147 Angle : 0.585 26.956 20719 Z= 0.307 Chirality : 0.039 0.194 2270 Planarity : 0.004 0.054 2589 Dihedral : 10.541 89.273 2314 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.76 (0.19), residues: 1784 helix: 0.61 (0.18), residues: 806 sheet: -0.63 (0.38), residues: 197 loop : -1.67 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.014 0.001 TYR A 334 PHE 0.021 0.001 PHE B 730 TRP 0.030 0.002 TRP A 406 HIS 0.007 0.001 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00310 (15287) covalent geometry : angle 0.58545 (20719) hydrogen bonds : bond 0.03822 ( 732) hydrogen bonds : angle 4.77722 ( 2015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4317.17 seconds wall clock time: 74 minutes 38.75 seconds (4478.75 seconds total)