Starting phenix.real_space_refine on Mon Aug 25 15:32:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nj7_12375/08_2025/7nj7_12375.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj7_12375/08_2025/7nj7_12375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nj7_12375/08_2025/7nj7_12375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj7_12375/08_2025/7nj7_12375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nj7_12375/08_2025/7nj7_12375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj7_12375/08_2025/7nj7_12375.map" } resolution = 4.82 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= 0.027 sd= 0.261 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 9336 2.51 5 N 2604 2.21 5 O 2881 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 28818 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: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 3 Time building chain proxies: 4.73, per 1000 atoms: 0.16 Number of scatterers: 28818 At special positions: 0 Unit cell: (102, 112, 174, 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 2881 8.00 N 2604 7.00 C 9336 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 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: 1.97 Conformation dependent library (CDL) restraints added in 894.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 18 sheets defined 49.7% alpha, 14.2% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.006A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.692A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.947A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.778A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.827A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.588A 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: 3.977A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.108A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A 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: 3.747A 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: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.618A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 62 through 65 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: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.537A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A 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: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.690A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A 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: 6.929A 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: 7.164A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.662A 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: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.174A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.517A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.634A 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: 5.973A 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 11 removed outlier: 6.836A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 97 through 98 727 hydrogen bonds defined for protein. 1986 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: 5.45 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13841 1.03 - 1.23: 426 1.23 - 1.43: 6047 1.43 - 1.63: 8669 1.63 - 1.83: 183 Bond restraints: 29166 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.511 -0.053 1.40e-02 5.10e+03 1.41e+01 bond pdb=" CD ARG F 61 " pdb=" NE ARG F 61 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.16e+01 bond pdb=" CD ARG F 72 " pdb=" NE ARG F 72 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" CD ARG F 50 " pdb=" NE ARG F 50 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.40e-02 5.10e+03 9.97e+00 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 9.84e+00 ... (remaining 29161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 52308 5.64 - 11.27: 15 11.27 - 16.91: 0 16.91 - 22.55: 1 22.55 - 28.19: 5 Bond angle restraints: 52329 Sorted by residual: angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 108.00 79.81 28.19 3.00e+00 1.11e-01 8.83e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.32 27.68 3.00e+00 1.11e-01 8.52e+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 81.81 27.19 3.00e+00 1.11e-01 8.22e+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 82.44 26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.75 -26.85 3.20e+00 9.77e-02 7.04e+01 ... (remaining 52324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12579 17.94 - 35.88: 866 35.88 - 53.83: 260 53.83 - 71.77: 88 71.77 - 89.71: 18 Dihedral angle restraints: 13811 sinusoidal: 7748 harmonic: 6063 Sorted by residual: dihedral pdb=" CA ALA F 35 " pdb=" C ALA F 35 " pdb=" N TRP F 36 " pdb=" CA TRP F 36 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ARG F 72 " pdb=" C ARG F 72 " pdb=" N ASP F 73 " pdb=" CA ASP F 73 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS F 76 " pdb=" C LYS F 76 " pdb=" N ASN F 77 " pdb=" CA ASN F 77 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 13808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1880 0.050 - 0.100: 295 0.100 - 0.149: 75 0.149 - 0.199: 20 0.199 - 0.249: 6 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA VAL F 2 " pdb=" N VAL F 2 " pdb=" C VAL F 2 " pdb=" CB VAL F 2 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU F 51 " pdb=" N LEU F 51 " pdb=" C LEU F 51 " pdb=" CB LEU F 51 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 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 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2273 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 38 " -0.475 9.50e-02 1.11e+02 2.13e-01 2.83e+01 pdb=" NE ARG F 38 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG F 38 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG F 38 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 38 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 68 " 0.057 2.00e-02 2.50e+03 3.72e-02 2.42e+01 pdb=" CG PHE F 68 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE F 68 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE F 68 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE F 68 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE F 68 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 68 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 95 " 0.062 2.00e-02 2.50e+03 3.22e-02 2.07e+01 pdb=" CG TYR F 95 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 95 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR F 95 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR F 95 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 95 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 95 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR F 95 " 0.041 2.00e-02 2.50e+03 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1260 2.17 - 2.78: 56237 2.78 - 3.39: 80883 3.39 - 3.99: 105856 3.99 - 4.60: 165095 Nonbonded interactions: 409331 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 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 2.450 ... (remaining 409326 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: 0.100 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4810 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 0.054 15299 Z= 0.236 Angle : 0.727 26.848 20738 Z= 0.430 Chirality : 0.044 0.249 2276 Planarity : 0.007 0.213 2590 Dihedral : 14.448 89.712 5986 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1781 helix: 0.46 (0.19), residues: 786 sheet: -0.72 (0.36), residues: 188 loop : -1.31 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 72 TYR 0.062 0.002 TYR F 95 PHE 0.057 0.002 PHE F 68 TRP 0.030 0.002 TRP F 36 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00434 (15298) covalent geometry : angle 0.72724 (20736) SS BOND : bond 0.01177 ( 1) SS BOND : angle 1.92260 ( 2) hydrogen bonds : bond 0.14986 ( 732) hydrogen bonds : angle 5.89777 ( 2006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 365 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 362 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 PHE cc_start: 0.6581 (t80) cc_final: 0.6232 (t80) REVERT: A 282 PHE cc_start: 0.7150 (p90) cc_final: 0.6681 (p90) REVERT: A 334 TYR cc_start: 0.7534 (m-80) cc_final: 0.6598 (m-10) REVERT: A 483 ILE cc_start: 0.8212 (mt) cc_final: 0.8008 (tp) REVERT: A 545 ILE cc_start: 0.5896 (pt) cc_final: 0.5619 (pt) REVERT: A 581 MET cc_start: 0.7677 (mtp) cc_final: 0.6784 (mtp) REVERT: A 585 LEU cc_start: 0.7686 (mt) cc_final: 0.7309 (tp) REVERT: A 648 SER cc_start: 0.9248 (t) cc_final: 0.9038 (m) REVERT: A 667 LEU cc_start: 0.8988 (mt) cc_final: 0.8471 (mt) REVERT: B 223 THR cc_start: 0.7027 (t) cc_final: 0.6776 (t) REVERT: B 236 LEU cc_start: 0.8817 (tp) cc_final: 0.8510 (pt) REVERT: B 261 SER cc_start: 0.8474 (m) cc_final: 0.8251 (p) REVERT: B 519 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7423 (tt0) REVERT: B 609 VAL cc_start: 0.7594 (t) cc_final: 0.7263 (t) REVERT: B 657 TYR cc_start: 0.8327 (p90) cc_final: 0.7371 (p90) REVERT: C 49 TRP cc_start: 0.7612 (t-100) cc_final: 0.7081 (t60) REVERT: C 90 MET cc_start: 0.3847 (mtm) cc_final: 0.3602 (ptp) REVERT: C 192 GLU cc_start: 0.7969 (tp30) cc_final: 0.7618 (tp30) REVERT: C 232 LEU cc_start: 0.6663 (tp) cc_final: 0.6136 (tt) REVERT: C 240 TRP cc_start: 0.6411 (p-90) cc_final: 0.5866 (p-90) outliers start: 3 outliers final: 1 residues processed: 365 average time/residue: 0.3080 time to fit residues: 157.4814 Evaluate side-chains 256 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN B 756 GLN C 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.127885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.108576 restraints weight = 196739.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.113625 restraints weight = 101966.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.116844 restraints weight = 59109.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.118909 restraints weight = 37840.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.120066 restraints weight = 26544.041| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5500 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15299 Z= 0.191 Angle : 0.641 27.595 20738 Z= 0.344 Chirality : 0.040 0.189 2276 Planarity : 0.005 0.067 2590 Dihedral : 10.168 73.403 2313 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.19), residues: 1781 helix: 0.38 (0.18), residues: 781 sheet: -0.43 (0.38), residues: 191 loop : -1.29 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 663 TYR 0.018 0.002 TYR B 217 PHE 0.030 0.002 PHE A 446 TRP 0.016 0.002 TRP B 613 HIS 0.009 0.001 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00394 (15298) covalent geometry : angle 0.64071 (20736) SS BOND : bond 0.00453 ( 1) SS BOND : angle 1.70475 ( 2) hydrogen bonds : bond 0.04673 ( 732) hydrogen bonds : angle 5.05803 ( 2006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 289 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.0223 (ppp) cc_final: -0.0106 (ppp) REVERT: A 260 PHE cc_start: 0.7573 (t80) cc_final: 0.6641 (t80) REVERT: A 459 ILE cc_start: 0.5726 (mt) cc_final: 0.5251 (mt) REVERT: A 477 MET cc_start: 0.4655 (mtp) cc_final: 0.4190 (ptp) REVERT: A 581 MET cc_start: 0.8493 (mtp) cc_final: 0.7542 (mtp) REVERT: A 585 LEU cc_start: 0.7717 (mt) cc_final: 0.7435 (tp) REVERT: A 661 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7511 (mm-30) REVERT: B 40 MET cc_start: 0.8737 (mtp) cc_final: 0.7958 (ttp) REVERT: B 179 MET cc_start: 0.2214 (mtt) cc_final: 0.1400 (mtt) REVERT: B 317 MET cc_start: 0.8829 (ttm) cc_final: 0.8534 (tpp) REVERT: B 389 ILE cc_start: 0.8709 (mt) cc_final: 0.8284 (mt) REVERT: B 407 MET cc_start: 0.8420 (tpp) cc_final: 0.8217 (tpp) REVERT: B 532 ASN cc_start: 0.8435 (m-40) cc_final: 0.8234 (m-40) REVERT: B 572 ARG cc_start: 0.6737 (mmm160) cc_final: 0.6367 (mmm160) REVERT: B 620 TYR cc_start: 0.7230 (t80) cc_final: 0.5698 (t80) REVERT: B 657 TYR cc_start: 0.8555 (p90) cc_final: 0.7939 (p90) REVERT: B 688 MET cc_start: 0.8766 (mmp) cc_final: 0.8530 (mmm) REVERT: B 744 MET cc_start: 0.4943 (ptm) cc_final: 0.4722 (ppp) REVERT: C 49 TRP cc_start: 0.9006 (t-100) cc_final: 0.8026 (t60) REVERT: C 50 MET cc_start: 0.8537 (ptm) cc_final: 0.7903 (tpp) REVERT: C 90 MET cc_start: 0.5072 (mtm) cc_final: 0.4582 (ptt) REVERT: C 172 VAL cc_start: 0.8651 (p) cc_final: 0.8389 (p) REVERT: F 34 MET cc_start: -0.2610 (mmt) cc_final: -0.3653 (tmm) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2667 time to fit residues: 109.6078 Evaluate side-chains 237 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 27 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS B 134 ASN B 313 GLN B 425 ASN B 537 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.120753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.101622 restraints weight = 202716.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.106228 restraints weight = 105030.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.109246 restraints weight = 61643.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.111212 restraints weight = 40183.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.112391 restraints weight = 28717.926| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15299 Z= 0.199 Angle : 0.638 24.990 20738 Z= 0.341 Chirality : 0.039 0.174 2276 Planarity : 0.005 0.060 2590 Dihedral : 10.131 73.354 2313 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.19), residues: 1781 helix: 0.27 (0.18), residues: 794 sheet: -0.47 (0.37), residues: 205 loop : -1.42 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 638 TYR 0.013 0.002 TYR B 217 PHE 0.021 0.002 PHE B 730 TRP 0.019 0.002 TRP C 99 HIS 0.010 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00409 (15298) covalent geometry : angle 0.63770 (20736) SS BOND : bond 0.00625 ( 1) SS BOND : angle 1.79870 ( 2) hydrogen bonds : bond 0.04420 ( 732) hydrogen bonds : angle 5.06358 ( 2006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 263 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.3491 (m-80) cc_final: 0.2690 (m-80) REVERT: A 477 MET cc_start: 0.5640 (mtp) cc_final: 0.5129 (ptm) REVERT: A 543 LEU cc_start: 0.9280 (mt) cc_final: 0.9011 (mt) REVERT: A 563 LEU cc_start: 0.6407 (tp) cc_final: 0.6060 (tp) REVERT: A 581 MET cc_start: 0.8334 (mtp) cc_final: 0.7325 (mtp) REVERT: A 585 LEU cc_start: 0.8040 (mt) cc_final: 0.7229 (tp) REVERT: B 40 MET cc_start: 0.8858 (mtp) cc_final: 0.7870 (ttm) REVERT: B 171 MET cc_start: 0.5614 (ptp) cc_final: 0.5196 (ptp) REVERT: B 179 MET cc_start: 0.1410 (mtt) cc_final: 0.0594 (mtt) REVERT: B 313 GLN cc_start: 0.5555 (OUTLIER) cc_final: 0.5092 (mt0) REVERT: B 411 MET cc_start: 0.8316 (mmm) cc_final: 0.7290 (mmm) REVERT: B 657 TYR cc_start: 0.8630 (p90) cc_final: 0.7931 (p90) REVERT: B 688 MET cc_start: 0.8920 (mmp) cc_final: 0.8553 (mmm) REVERT: C 49 TRP cc_start: 0.9151 (t-100) cc_final: 0.8361 (t60) REVERT: C 50 MET cc_start: 0.8467 (ptm) cc_final: 0.7993 (tpp) REVERT: C 51 MET cc_start: 0.8857 (tpp) cc_final: 0.8656 (tpp) REVERT: C 67 ILE cc_start: 0.7721 (mt) cc_final: 0.7513 (tt) REVERT: C 172 VAL cc_start: 0.8948 (p) cc_final: 0.8238 (m) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.2568 time to fit residues: 98.0562 Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 0.0170 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 151 optimal weight: 0.3980 chunk 67 optimal weight: 10.0000 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN B 425 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN C 82 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.120509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.101456 restraints weight = 202974.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.106100 restraints weight = 104071.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.109047 restraints weight = 60708.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.110963 restraints weight = 39786.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.112280 restraints weight = 28610.488| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15299 Z= 0.135 Angle : 0.564 27.566 20738 Z= 0.299 Chirality : 0.038 0.160 2276 Planarity : 0.005 0.097 2590 Dihedral : 10.025 73.258 2313 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.19), residues: 1781 helix: 0.46 (0.18), residues: 792 sheet: -0.47 (0.36), residues: 206 loop : -1.27 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 151 TYR 0.014 0.001 TYR B 497 PHE 0.038 0.002 PHE B 501 TRP 0.010 0.001 TRP B 613 HIS 0.009 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00289 (15298) covalent geometry : angle 0.56373 (20736) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.61305 ( 2) hydrogen bonds : bond 0.03971 ( 732) hydrogen bonds : angle 4.78555 ( 2006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 249 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.654 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: A 543 LEU cc_start: 0.9252 (mt) cc_final: 0.8975 (mt) REVERT: A 579 MET cc_start: 0.8611 (tmm) cc_final: 0.7546 (ttt) REVERT: A 581 MET cc_start: 0.8290 (mtp) cc_final: 0.7263 (mtp) REVERT: A 585 LEU cc_start: 0.7994 (mt) cc_final: 0.7019 (tp) REVERT: A 589 LEU cc_start: 0.8428 (mm) cc_final: 0.8086 (mm) REVERT: A 591 GLN cc_start: 0.9380 (tm-30) cc_final: 0.9137 (tm-30) REVERT: B 40 MET cc_start: 0.8757 (mtp) cc_final: 0.8004 (ttp) REVERT: B 348 MET cc_start: 0.6578 (mmp) cc_final: 0.5795 (mmt) REVERT: B 407 MET cc_start: 0.8706 (tpp) cc_final: 0.8318 (tpp) REVERT: B 411 MET cc_start: 0.8324 (mmm) cc_final: 0.7077 (mmm) REVERT: B 551 PHE cc_start: 0.7734 (t80) cc_final: 0.7518 (t80) REVERT: B 645 MET cc_start: 0.7913 (mpp) cc_final: 0.7236 (mpp) REVERT: B 657 TYR cc_start: 0.8544 (p90) cc_final: 0.8021 (p90) REVERT: B 688 MET cc_start: 0.8941 (mmp) cc_final: 0.8600 (mmm) REVERT: B 692 CYS cc_start: 0.7733 (m) cc_final: 0.7506 (p) REVERT: B 718 MET cc_start: 0.8675 (mtt) cc_final: 0.8129 (mmm) REVERT: C 49 TRP cc_start: 0.9112 (t-100) cc_final: 0.8801 (t60) REVERT: C 67 ILE cc_start: 0.7976 (mt) cc_final: 0.7670 (tt) REVERT: C 164 MET cc_start: 0.8906 (tpt) cc_final: 0.8591 (tpp) REVERT: C 172 VAL cc_start: 0.8730 (p) cc_final: 0.8053 (p) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2590 time to fit residues: 93.1511 Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN B 292 ASN B 425 ASN B 569 GLN C 127 HIS F 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.112618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.093590 restraints weight = 207825.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.097887 restraints weight = 107597.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.100700 restraints weight = 64578.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.102477 restraints weight = 43070.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.103716 restraints weight = 31647.914| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15299 Z= 0.226 Angle : 0.664 25.991 20738 Z= 0.359 Chirality : 0.039 0.153 2276 Planarity : 0.006 0.113 2590 Dihedral : 10.274 76.738 2313 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.19), residues: 1781 helix: -0.11 (0.17), residues: 799 sheet: -0.74 (0.36), residues: 204 loop : -1.65 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 566 TYR 0.016 0.002 TYR B 705 PHE 0.024 0.002 PHE B 412 TRP 0.026 0.002 TRP B 613 HIS 0.007 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00456 (15298) covalent geometry : angle 0.66362 (20736) SS BOND : bond 0.00632 ( 1) SS BOND : angle 1.34873 ( 2) hydrogen bonds : bond 0.04381 ( 732) hydrogen bonds : angle 5.28949 ( 2006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.8481 (m-80) cc_final: 0.7643 (m-10) REVERT: A 389 ASP cc_start: 0.5326 (t0) cc_final: 0.4758 (t70) REVERT: A 459 ILE cc_start: 0.7884 (mt) cc_final: 0.6784 (mt) REVERT: A 543 LEU cc_start: 0.9373 (mt) cc_final: 0.9040 (mt) REVERT: A 581 MET cc_start: 0.8417 (mtp) cc_final: 0.7410 (mtp) REVERT: A 585 LEU cc_start: 0.7949 (mt) cc_final: 0.6766 (tp) REVERT: A 641 LEU cc_start: 0.7047 (tp) cc_final: 0.6825 (tp) REVERT: B 40 MET cc_start: 0.8934 (mtp) cc_final: 0.8142 (ttp) REVERT: B 224 LEU cc_start: 0.7796 (mt) cc_final: 0.7507 (mt) REVERT: B 347 LYS cc_start: 0.8550 (pttm) cc_final: 0.8025 (pttm) REVERT: B 411 MET cc_start: 0.8393 (mmm) cc_final: 0.7431 (mmm) REVERT: B 412 PHE cc_start: 0.9043 (m-10) cc_final: 0.8792 (m-80) REVERT: B 425 ASN cc_start: 0.9312 (t160) cc_final: 0.8958 (t0) REVERT: B 519 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8604 (mp0) REVERT: B 522 ASP cc_start: 0.7625 (m-30) cc_final: 0.7422 (t70) REVERT: B 576 ILE cc_start: 0.7115 (mt) cc_final: 0.6896 (mt) REVERT: B 645 MET cc_start: 0.8194 (mpp) cc_final: 0.7285 (mpp) REVERT: B 657 TYR cc_start: 0.8531 (p90) cc_final: 0.8159 (p90) REVERT: B 688 MET cc_start: 0.9056 (mmp) cc_final: 0.8827 (mmm) REVERT: C 50 MET cc_start: 0.8913 (tpp) cc_final: 0.8596 (tpp) REVERT: C 53 MET cc_start: 0.7004 (ttt) cc_final: 0.6641 (ttm) REVERT: C 67 ILE cc_start: 0.8170 (mt) cc_final: 0.7889 (tt) REVERT: C 164 MET cc_start: 0.8916 (tpt) cc_final: 0.8582 (tpp) REVERT: C 232 LEU cc_start: 0.8015 (tp) cc_final: 0.7777 (tp) REVERT: F 34 MET cc_start: -0.2282 (mmt) cc_final: -0.3226 (tmm) outliers start: 1 outliers final: 1 residues processed: 247 average time/residue: 0.2450 time to fit residues: 89.3634 Evaluate side-chains 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 10 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 chunk 170 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 425 ASN B 582 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.113937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.094749 restraints weight = 202804.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.099216 restraints weight = 104684.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.102001 restraints weight = 61804.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.103890 restraints weight = 41245.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.105182 restraints weight = 30021.461| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15299 Z= 0.129 Angle : 0.551 26.523 20738 Z= 0.292 Chirality : 0.038 0.164 2276 Planarity : 0.004 0.060 2590 Dihedral : 10.128 78.748 2313 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.19), residues: 1781 helix: 0.35 (0.18), residues: 795 sheet: -0.69 (0.37), residues: 204 loop : -1.39 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 443 TYR 0.014 0.001 TYR A 464 PHE 0.030 0.001 PHE B 631 TRP 0.011 0.001 TRP C 240 HIS 0.005 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00271 (15298) covalent geometry : angle 0.55104 (20736) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.55677 ( 2) hydrogen bonds : bond 0.03792 ( 732) hydrogen bonds : angle 4.84473 ( 2006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.8470 (m-80) cc_final: 0.7703 (m-10) REVERT: A 389 ASP cc_start: 0.5044 (t0) cc_final: 0.4504 (t70) REVERT: A 459 ILE cc_start: 0.7765 (mt) cc_final: 0.6693 (mt) REVERT: A 477 MET cc_start: 0.6730 (mtp) cc_final: 0.5793 (ptt) REVERT: A 543 LEU cc_start: 0.9325 (mt) cc_final: 0.8961 (mt) REVERT: A 579 MET cc_start: 0.8898 (tmm) cc_final: 0.7828 (ttt) REVERT: A 581 MET cc_start: 0.8310 (mtp) cc_final: 0.7312 (mtp) REVERT: A 585 LEU cc_start: 0.8213 (mt) cc_final: 0.6954 (tp) REVERT: B 40 MET cc_start: 0.8953 (mtp) cc_final: 0.8093 (ttp) REVERT: B 224 LEU cc_start: 0.7845 (mt) cc_final: 0.7541 (mt) REVERT: B 317 MET cc_start: 0.9124 (tpp) cc_final: 0.8907 (mmt) REVERT: B 347 LYS cc_start: 0.8402 (pttm) cc_final: 0.7424 (pttm) REVERT: B 348 MET cc_start: 0.6607 (mmp) cc_final: 0.5720 (mmt) REVERT: B 407 MET cc_start: 0.8894 (tpp) cc_final: 0.8595 (tpp) REVERT: B 411 MET cc_start: 0.8378 (mmm) cc_final: 0.7275 (mmm) REVERT: B 412 PHE cc_start: 0.8967 (m-10) cc_final: 0.8737 (m-80) REVERT: B 425 ASN cc_start: 0.9319 (t160) cc_final: 0.8884 (t0) REVERT: B 551 PHE cc_start: 0.8434 (t80) cc_final: 0.8077 (t80) REVERT: B 645 MET cc_start: 0.8220 (mpp) cc_final: 0.7268 (mpp) REVERT: B 657 TYR cc_start: 0.8731 (p90) cc_final: 0.8450 (p90) REVERT: B 688 MET cc_start: 0.9012 (mmp) cc_final: 0.8640 (mmp) REVERT: B 692 CYS cc_start: 0.8904 (m) cc_final: 0.8350 (p) REVERT: B 718 MET cc_start: 0.8774 (mtt) cc_final: 0.8319 (mmm) REVERT: C 49 TRP cc_start: 0.9321 (t-100) cc_final: 0.8510 (t60) REVERT: C 51 MET cc_start: 0.9093 (tpp) cc_final: 0.8720 (mmm) REVERT: C 53 MET cc_start: 0.6804 (ttt) cc_final: 0.6460 (ttm) REVERT: C 67 ILE cc_start: 0.8276 (mt) cc_final: 0.8042 (tt) REVERT: C 164 MET cc_start: 0.8898 (tpt) cc_final: 0.8535 (tpp) REVERT: F 34 MET cc_start: -0.0452 (mpp) cc_final: -0.1416 (mmm) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2605 time to fit residues: 92.6113 Evaluate side-chains 214 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 152 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 413 ASN B 425 ASN ** C 73 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 = 0.4188 r_free = 0.4188 target = 0.110557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.091442 restraints weight = 207052.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.095673 restraints weight = 107590.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.098441 restraints weight = 64496.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.100316 restraints weight = 43216.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.101532 restraints weight = 31609.523| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15299 Z= 0.176 Angle : 0.598 25.033 20738 Z= 0.321 Chirality : 0.039 0.194 2276 Planarity : 0.005 0.079 2590 Dihedral : 10.226 81.368 2313 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1781 helix: 0.19 (0.18), residues: 804 sheet: -0.88 (0.36), residues: 205 loop : -1.55 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 185 TYR 0.030 0.002 TYR B 82 PHE 0.021 0.002 PHE B 631 TRP 0.018 0.002 TRP B 613 HIS 0.007 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00362 (15298) covalent geometry : angle 0.59824 (20736) SS BOND : bond 0.00526 ( 1) SS BOND : angle 0.27466 ( 2) hydrogen bonds : bond 0.03879 ( 732) hydrogen bonds : angle 5.03330 ( 2006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 PHE cc_start: 0.6523 (t80) cc_final: 0.5863 (t80) REVERT: A 334 TYR cc_start: 0.8475 (m-80) cc_final: 0.7607 (m-10) REVERT: A 389 ASP cc_start: 0.5464 (t0) cc_final: 0.4900 (t0) REVERT: A 459 ILE cc_start: 0.7914 (mt) cc_final: 0.7630 (mt) REVERT: A 477 MET cc_start: 0.6819 (mtp) cc_final: 0.5649 (ptt) REVERT: A 543 LEU cc_start: 0.9380 (mt) cc_final: 0.9006 (mt) REVERT: A 579 MET cc_start: 0.8442 (tmm) cc_final: 0.7830 (ttt) REVERT: A 581 MET cc_start: 0.8379 (mtp) cc_final: 0.7406 (mtp) REVERT: A 672 LEU cc_start: 0.6739 (tp) cc_final: 0.6125 (tp) REVERT: B 40 MET cc_start: 0.9038 (mtp) cc_final: 0.8229 (ttp) REVERT: B 407 MET cc_start: 0.9050 (tpp) cc_final: 0.8591 (tpp) REVERT: B 411 MET cc_start: 0.8439 (mmm) cc_final: 0.7387 (mmm) REVERT: B 412 PHE cc_start: 0.9062 (m-10) cc_final: 0.8774 (m-80) REVERT: B 425 ASN cc_start: 0.9361 (t160) cc_final: 0.8983 (t0) REVERT: B 532 ASN cc_start: 0.8761 (m-40) cc_final: 0.8546 (m-40) REVERT: B 645 MET cc_start: 0.8266 (mpp) cc_final: 0.8041 (mpp) REVERT: B 657 TYR cc_start: 0.8719 (p90) cc_final: 0.8507 (p90) REVERT: B 688 MET cc_start: 0.9012 (mmp) cc_final: 0.8766 (mmp) REVERT: B 718 MET cc_start: 0.8801 (mtt) cc_final: 0.8303 (mmm) REVERT: C 50 MET cc_start: 0.9035 (tpp) cc_final: 0.8735 (tpp) REVERT: C 51 MET cc_start: 0.9175 (tpp) cc_final: 0.8612 (mmm) REVERT: C 53 MET cc_start: 0.6896 (ttt) cc_final: 0.6497 (ttm) REVERT: C 164 MET cc_start: 0.8928 (tpt) cc_final: 0.8572 (tpp) REVERT: F 34 MET cc_start: 0.0955 (mpp) cc_final: -0.0731 (mmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2618 time to fit residues: 90.0990 Evaluate side-chains 205 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 25 optimal weight: 9.9990 chunk 49 optimal weight: 0.0170 chunk 166 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 154 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 overall best weight: 2.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** C 73 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 = 0.4170 r_free = 0.4170 target = 0.109049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.090193 restraints weight = 208976.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.094348 restraints weight = 108466.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.097096 restraints weight = 64803.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.098940 restraints weight = 43212.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.099993 restraints weight = 31529.125| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15299 Z= 0.152 Angle : 0.579 27.145 20738 Z= 0.307 Chirality : 0.038 0.155 2276 Planarity : 0.005 0.068 2590 Dihedral : 10.247 84.210 2313 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.19), residues: 1781 helix: 0.31 (0.18), residues: 802 sheet: -0.87 (0.36), residues: 206 loop : -1.48 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 707 TYR 0.014 0.002 TYR B 82 PHE 0.018 0.002 PHE B 551 TRP 0.016 0.002 TRP C 240 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00319 (15298) covalent geometry : angle 0.57904 (20736) SS BOND : bond 0.00353 ( 1) SS BOND : angle 0.62400 ( 2) hydrogen bonds : bond 0.03792 ( 732) hydrogen bonds : angle 4.88942 ( 2006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.7765 (mpp) cc_final: 0.7420 (mtm) REVERT: A 214 LEU cc_start: 0.8534 (mt) cc_final: 0.8236 (mt) REVERT: A 260 PHE cc_start: 0.6605 (t80) cc_final: 0.5978 (t80) REVERT: A 389 ASP cc_start: 0.5777 (t0) cc_final: 0.5300 (t0) REVERT: A 436 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6867 (mt-10) REVERT: A 477 MET cc_start: 0.7290 (mtp) cc_final: 0.6166 (ptt) REVERT: A 543 LEU cc_start: 0.9392 (mt) cc_final: 0.9029 (mt) REVERT: A 579 MET cc_start: 0.8458 (tmm) cc_final: 0.7907 (ttt) REVERT: A 581 MET cc_start: 0.8409 (mtp) cc_final: 0.7372 (mtp) REVERT: A 672 LEU cc_start: 0.6885 (tp) cc_final: 0.6499 (tp) REVERT: B 40 MET cc_start: 0.9059 (mtp) cc_final: 0.8252 (ttp) REVERT: B 224 LEU cc_start: 0.7851 (mt) cc_final: 0.7632 (mt) REVERT: B 407 MET cc_start: 0.8983 (tpp) cc_final: 0.8716 (tpp) REVERT: B 414 MET cc_start: 0.3725 (mmm) cc_final: 0.3170 (mmt) REVERT: B 425 ASN cc_start: 0.9352 (t160) cc_final: 0.8528 (t0) REVERT: B 645 MET cc_start: 0.8116 (mpp) cc_final: 0.7320 (mpp) REVERT: B 688 MET cc_start: 0.9022 (mmp) cc_final: 0.8082 (mtt) REVERT: B 718 MET cc_start: 0.8819 (mtt) cc_final: 0.8301 (mmm) REVERT: C 49 TRP cc_start: 0.9388 (t-100) cc_final: 0.8591 (t60) REVERT: C 51 MET cc_start: 0.9108 (tpp) cc_final: 0.8698 (mmm) REVERT: C 53 MET cc_start: 0.6847 (ttt) cc_final: 0.6599 (ttt) REVERT: C 164 MET cc_start: 0.8929 (tpt) cc_final: 0.8562 (tpp) REVERT: F 34 MET cc_start: 0.1556 (mpp) cc_final: 0.1065 (mpp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2457 time to fit residues: 83.4858 Evaluate side-chains 207 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.110223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.091201 restraints weight = 204761.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.095466 restraints weight = 105323.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.098274 restraints weight = 62559.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.100175 restraints weight = 41454.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.101316 restraints weight = 30040.353| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15299 Z= 0.106 Angle : 0.535 25.932 20738 Z= 0.281 Chirality : 0.037 0.150 2276 Planarity : 0.004 0.051 2590 Dihedral : 10.139 85.016 2313 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.20), residues: 1781 helix: 0.70 (0.18), residues: 800 sheet: -0.79 (0.36), residues: 205 loop : -1.30 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 707 TYR 0.015 0.001 TYR B 30 PHE 0.018 0.001 PHE B 696 TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00230 (15298) covalent geometry : angle 0.53485 (20736) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.25490 ( 2) hydrogen bonds : bond 0.03526 ( 732) hydrogen bonds : angle 4.61931 ( 2006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.619 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 211 MET cc_start: 0.7731 (mpp) cc_final: 0.7260 (mtm) REVERT: A 214 LEU cc_start: 0.8427 (mt) cc_final: 0.8120 (mt) REVERT: A 260 PHE cc_start: 0.6543 (t80) cc_final: 0.5897 (t80) REVERT: A 334 TYR cc_start: 0.8577 (m-80) cc_final: 0.7705 (m-10) REVERT: A 389 ASP cc_start: 0.5669 (t0) cc_final: 0.5250 (t0) REVERT: A 436 GLU cc_start: 0.6303 (mt-10) cc_final: 0.6068 (mt-10) REVERT: A 543 LEU cc_start: 0.9380 (mt) cc_final: 0.9168 (mt) REVERT: A 579 MET cc_start: 0.8390 (tmm) cc_final: 0.7785 (ttt) REVERT: A 581 MET cc_start: 0.7984 (mtp) cc_final: 0.6772 (mtp) REVERT: A 672 LEU cc_start: 0.6803 (tp) cc_final: 0.6371 (tp) REVERT: B 40 MET cc_start: 0.9054 (mtp) cc_final: 0.8404 (ttm) REVERT: B 127 GLN cc_start: 0.6383 (mm110) cc_final: 0.5310 (mm110) REVERT: B 224 LEU cc_start: 0.7798 (mt) cc_final: 0.7418 (mt) REVERT: B 347 LYS cc_start: 0.8416 (pttm) cc_final: 0.7823 (pttm) REVERT: B 356 MET cc_start: 0.8966 (ttm) cc_final: 0.8644 (ttm) REVERT: B 407 MET cc_start: 0.9033 (tpp) cc_final: 0.8620 (tpp) REVERT: B 411 MET cc_start: 0.8637 (mmm) cc_final: 0.7724 (mmm) REVERT: B 414 MET cc_start: 0.3638 (mmm) cc_final: 0.3103 (mmt) REVERT: B 425 ASN cc_start: 0.9119 (t160) cc_final: 0.8579 (t0) REVERT: B 532 ASN cc_start: 0.8687 (m-40) cc_final: 0.8442 (m-40) REVERT: B 645 MET cc_start: 0.7971 (mpp) cc_final: 0.7146 (mpp) REVERT: B 688 MET cc_start: 0.8980 (mmp) cc_final: 0.8091 (mtt) REVERT: B 692 CYS cc_start: 0.8970 (m) cc_final: 0.8463 (p) REVERT: B 718 MET cc_start: 0.8979 (mtt) cc_final: 0.8464 (mmm) REVERT: C 50 MET cc_start: 0.8923 (tpp) cc_final: 0.8610 (tpp) REVERT: C 51 MET cc_start: 0.9070 (tpp) cc_final: 0.8720 (mmm) REVERT: C 53 MET cc_start: 0.6722 (ttt) cc_final: 0.6382 (ttm) REVERT: C 161 ASP cc_start: 0.8949 (m-30) cc_final: 0.8713 (p0) REVERT: C 164 MET cc_start: 0.8898 (tpt) cc_final: 0.8531 (tpp) REVERT: F 34 MET cc_start: 0.1407 (mpp) cc_final: 0.0982 (mpp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2578 time to fit residues: 88.2134 Evaluate side-chains 209 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 50 optimal weight: 0.0470 chunk 158 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 1.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.109694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.090844 restraints weight = 205050.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.095097 restraints weight = 105094.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.097847 restraints weight = 62392.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099711 restraints weight = 41592.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.100935 restraints weight = 30357.082| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15299 Z= 0.112 Angle : 0.534 26.347 20738 Z= 0.281 Chirality : 0.037 0.163 2276 Planarity : 0.004 0.055 2590 Dihedral : 10.103 86.186 2313 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.20), residues: 1781 helix: 0.76 (0.18), residues: 804 sheet: -0.72 (0.36), residues: 205 loop : -1.25 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 707 TYR 0.012 0.001 TYR B 82 PHE 0.027 0.001 PHE B 501 TRP 0.008 0.001 TRP C 240 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00242 (15298) covalent geometry : angle 0.53383 (20736) SS BOND : bond 0.00362 ( 1) SS BOND : angle 0.47763 ( 2) hydrogen bonds : bond 0.03482 ( 732) hydrogen bonds : angle 4.60941 ( 2006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 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 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.795 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 214 LEU cc_start: 0.8434 (mt) cc_final: 0.8157 (mt) REVERT: A 260 PHE cc_start: 0.6511 (t80) cc_final: 0.5872 (t80) REVERT: A 389 ASP cc_start: 0.5759 (t0) cc_final: 0.5326 (t0) REVERT: A 436 GLU cc_start: 0.6737 (mt-10) cc_final: 0.5951 (tt0) REVERT: A 477 MET cc_start: 0.7025 (mtp) cc_final: 0.5334 (ttp) REVERT: A 543 LEU cc_start: 0.9371 (mt) cc_final: 0.9010 (mt) REVERT: A 579 MET cc_start: 0.8433 (tmm) cc_final: 0.7821 (ttt) REVERT: A 581 MET cc_start: 0.8019 (mtp) cc_final: 0.6790 (mtp) REVERT: A 672 LEU cc_start: 0.6853 (tp) cc_final: 0.6423 (tp) REVERT: B 40 MET cc_start: 0.9047 (mtp) cc_final: 0.8216 (ttp) REVERT: B 127 GLN cc_start: 0.6244 (mm110) cc_final: 0.5264 (mm110) REVERT: B 224 LEU cc_start: 0.7792 (mt) cc_final: 0.7512 (mt) REVERT: B 347 LYS cc_start: 0.8441 (pttm) cc_final: 0.7813 (pttm) REVERT: B 407 MET cc_start: 0.9081 (tpp) cc_final: 0.8651 (tpp) REVERT: B 411 MET cc_start: 0.8660 (mmm) cc_final: 0.7759 (mmm) REVERT: B 414 MET cc_start: 0.3715 (mmm) cc_final: 0.3107 (mmt) REVERT: B 425 ASN cc_start: 0.9162 (t160) cc_final: 0.8844 (t0) REVERT: B 645 MET cc_start: 0.8214 (mpp) cc_final: 0.7173 (mpp) REVERT: B 657 TYR cc_start: 0.8239 (p90) cc_final: 0.7611 (p90) REVERT: B 688 MET cc_start: 0.8985 (mmp) cc_final: 0.8089 (mtt) REVERT: B 692 CYS cc_start: 0.8991 (m) cc_final: 0.8530 (p) REVERT: B 714 MET cc_start: 0.9284 (mtt) cc_final: 0.8867 (mmp) REVERT: B 718 MET cc_start: 0.8980 (mtt) cc_final: 0.8431 (mmm) REVERT: C 50 MET cc_start: 0.8904 (tpp) cc_final: 0.8620 (tpp) REVERT: C 51 MET cc_start: 0.9128 (tpp) cc_final: 0.8731 (mmm) REVERT: C 53 MET cc_start: 0.6613 (ttt) cc_final: 0.6289 (ttm) REVERT: C 161 ASP cc_start: 0.8963 (m-30) cc_final: 0.8723 (p0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2561 time to fit residues: 85.2899 Evaluate side-chains 209 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 83 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS B 425 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.106362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.087612 restraints weight = 210679.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.091652 restraints weight = 109142.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.094300 restraints weight = 65696.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.096085 restraints weight = 44206.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.097293 restraints weight = 32640.305| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 15299 Z= 0.167 Angle : 0.584 26.007 20738 Z= 0.311 Chirality : 0.038 0.155 2276 Planarity : 0.005 0.076 2590 Dihedral : 10.215 88.070 2313 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.19), residues: 1781 helix: 0.56 (0.18), residues: 798 sheet: -0.84 (0.36), residues: 205 loop : -1.42 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 707 TYR 0.018 0.002 TYR F 114 PHE 0.021 0.002 PHE B 551 TRP 0.017 0.002 TRP B 613 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00354 (15298) covalent geometry : angle 0.58433 (20736) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.53593 ( 2) hydrogen bonds : bond 0.03684 ( 732) hydrogen bonds : angle 4.82136 ( 2006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.95 seconds wall clock time: 74 minutes 41.93 seconds (4481.93 seconds total)