Starting phenix.real_space_refine on Wed Mar 20 22:53:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj5_12373/03_2024/7nj5_12373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj5_12373/03_2024/7nj5_12373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj5_12373/03_2024/7nj5_12373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj5_12373/03_2024/7nj5_12373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj5_12373/03_2024/7nj5_12373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj5_12373/03_2024/7nj5_12373.pdb" } resolution = 4.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 0.275 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 106 5.16 5 C 9327 2.51 5 N 2602 2.21 5 O 2880 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28806 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 11704 Classifications: {'peptide': 735} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4075 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "F" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 96} Chain breaks: 3 Time building chain proxies: 12.93, per 1000 atoms: 0.45 Number of scatterers: 28806 At special positions: 0 Unit cell: (102, 110, 162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 23 15.00 O 2880 8.00 N 2602 7.00 C 9327 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.00 Conformation dependent library (CDL) restraints added in 3.1 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.4% alpha, 15.5% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 13.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.141A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.005A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.691A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.946A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.638A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.635A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.733A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.778A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.530A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.826A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.587A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.510A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.036A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.330A pdb=" N GLY B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.978A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.893A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.522A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.746A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.585A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.658A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.619A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.513A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 146 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.536A pdb=" N LEU A 290 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.691A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.173A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.516A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.635A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.520A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.974A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.161A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER F 124 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL F 12 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL F 121 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL F 93 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 33 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.161A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER F 124 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL F 12 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL F 121 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL F 93 " --> pdb=" O VAL F 121 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 12.98 Time building geometry restraints manager: 22.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13841 1.04 - 1.23: 646 1.23 - 1.43: 5875 1.43 - 1.63: 8610 1.63 - 1.83: 183 Bond restraints: 29155 Sorted by residual: bond pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " ideal model delta sigma weight residual 1.458 1.522 -0.064 1.40e-02 5.10e+03 2.12e+01 bond pdb=" CE1 HIS F 59 " pdb=" NE2 HIS F 59 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.21e+01 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" CD ARG F 19 " pdb=" NE ARG F 19 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.40e-02 5.10e+03 9.96e+00 bond pdb=" C GLU A 677 " pdb=" O GLU A 677 " ideal model delta sigma weight residual 1.235 1.223 0.012 4.70e-03 4.53e+04 6.44e+00 ... (remaining 29150 not shown) Histogram of bond angle deviations from ideal: 79.76 - 91.56: 4 91.56 - 103.36: 203 103.36 - 115.16: 36417 115.16 - 126.96: 15448 126.96 - 138.76: 240 Bond angle restraints: 52312 Sorted by residual: angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 108.00 79.76 28.24 3.00e+00 1.11e-01 8.86e+01 angle pdb=" NZ LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 108.00 80.35 27.65 3.00e+00 1.11e-01 8.50e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE3 LYS A 113 " ideal model delta sigma weight residual 109.00 81.83 27.17 3.00e+00 1.11e-01 8.20e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" HE2 LYS A 113 " ideal model delta sigma weight residual 109.00 82.45 26.55 3.00e+00 1.11e-01 7.83e+01 angle pdb=" CD LYS A 113 " pdb=" CE LYS A 113 " pdb=" NZ LYS A 113 " ideal model delta sigma weight residual 111.90 138.76 -26.86 3.20e+00 9.77e-02 7.05e+01 ... (remaining 52307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12573 17.93 - 35.85: 859 35.85 - 53.78: 253 53.78 - 71.71: 89 71.71 - 89.63: 17 Dihedral angle restraints: 13791 sinusoidal: 7729 harmonic: 6062 Sorted by residual: dihedral pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual 122.80 137.99 -15.19 0 2.50e+00 1.60e-01 3.69e+01 dihedral pdb=" C SER F 85 " pdb=" N SER F 85 " pdb=" CA SER F 85 " pdb=" CB SER F 85 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 13788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2205 0.112 - 0.225: 58 0.225 - 0.337: 4 0.337 - 0.450: 2 0.450 - 0.562: 1 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CA SER F 85 " pdb=" N SER F 85 " pdb=" C SER F 85 " pdb=" CB SER F 85 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA ASN F 77 " pdb=" N ASN F 77 " pdb=" C ASN F 77 " pdb=" CB ASN F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA LYS F 65 " pdb=" N LYS F 65 " pdb=" C LYS F 65 " pdb=" CB LYS F 65 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 2267 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 94 " -0.017 2.00e-02 2.50e+03 4.95e-02 4.90e+01 pdb=" CG TYR F 94 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 94 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 94 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR F 94 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR F 94 " 0.062 2.00e-02 2.50e+03 pdb=" OH TYR F 94 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " 0.017 2.00e-02 2.50e+03 4.83e-02 4.67e+01 pdb=" CG TYR F 32 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 115 " 0.070 2.00e-02 2.50e+03 3.40e-02 2.89e+01 pdb=" CG TRP F 115 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP F 115 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP F 115 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP F 115 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP F 115 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 115 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 115 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 115 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP F 115 " 0.031 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1262 2.17 - 2.78: 56261 2.78 - 3.39: 80851 3.39 - 3.99: 105858 3.99 - 4.60: 165202 Nonbonded interactions: 409434 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.567 1.850 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.569 1.850 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.594 1.850 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.602 1.850 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.621 1.850 ... (remaining 409429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.080 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: 0.460 Extract box with map and model: 2.190 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 100.640 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15287 Z= 0.272 Angle : 0.731 26.860 20719 Z= 0.431 Chirality : 0.046 0.562 2270 Planarity : 0.005 0.090 2589 Dihedral : 14.354 89.632 5973 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.32 % Allowed : 0.25 % Favored : 99.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1784 helix: 0.45 (0.19), residues: 786 sheet: -0.71 (0.36), residues: 183 loop : -1.31 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP F 115 HIS 0.003 0.001 HIS A 41 PHE 0.048 0.002 PHE A 446 TYR 0.094 0.003 TYR F 94 ARG 0.034 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 402 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 ILE cc_start: 0.8127 (mt) cc_final: 0.7813 (tp) REVERT: A 522 SER cc_start: 0.8326 (m) cc_final: 0.8072 (t) REVERT: A 528 THR cc_start: 0.7469 (m) cc_final: 0.7145 (p) REVERT: A 633 ILE cc_start: 0.6114 (tt) cc_final: 0.5743 (tp) REVERT: A 648 SER cc_start: 0.9094 (t) cc_final: 0.8487 (m) REVERT: B 40 MET cc_start: 0.8049 (mtm) cc_final: 0.7434 (mtm) REVERT: B 229 LYS cc_start: 0.8336 (tttp) cc_final: 0.8097 (ttmm) REVERT: B 407 MET cc_start: 0.6422 (mmm) cc_final: 0.5894 (tpp) REVERT: B 446 ASP cc_start: 0.9092 (m-30) cc_final: 0.8684 (m-30) REVERT: B 509 LEU cc_start: 0.9586 (tp) cc_final: 0.9374 (tp) REVERT: B 561 CYS cc_start: 0.5949 (p) cc_final: 0.5054 (p) REVERT: B 568 ILE cc_start: 0.8315 (mt) cc_final: 0.7801 (tt) REVERT: B 612 LYS cc_start: 0.7594 (mttt) cc_final: 0.6572 (mttt) REVERT: C 42 ASN cc_start: 0.8592 (t0) cc_final: 0.7402 (p0) REVERT: F 12 VAL cc_start: -0.2206 (OUTLIER) cc_final: -0.2689 (m) outliers start: 5 outliers final: 1 residues processed: 406 average time/residue: 0.6299 time to fit residues: 364.7569 Evaluate side-chains 263 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 605 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN C 110 HIS F 59 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 15287 Z= 0.429 Angle : 0.827 27.827 20719 Z= 0.450 Chirality : 0.043 0.172 2270 Planarity : 0.006 0.072 2589 Dihedral : 10.559 73.589 2314 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 1784 helix: -0.61 (0.17), residues: 795 sheet: -0.79 (0.35), residues: 200 loop : -1.60 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 99 HIS 0.019 0.003 HIS C 110 PHE 0.027 0.003 PHE B 730 TYR 0.041 0.003 TYR B 217 ARG 0.052 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 268 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.7151 (m-80) cc_final: 0.6486 (m-80) REVERT: A 477 MET cc_start: 0.8526 (pmm) cc_final: 0.8048 (pmm) REVERT: A 513 ASN cc_start: 0.8683 (m-40) cc_final: 0.8480 (m-40) REVERT: A 528 THR cc_start: 0.8006 (m) cc_final: 0.7672 (p) REVERT: A 540 TYR cc_start: 0.7605 (m-80) cc_final: 0.7377 (m-80) REVERT: A 579 MET cc_start: 0.7876 (tmm) cc_final: 0.7663 (tmm) REVERT: B 3 VAL cc_start: 0.6477 (t) cc_final: 0.6016 (t) REVERT: B 356 MET cc_start: 0.7452 (ttm) cc_final: 0.7230 (ttm) REVERT: B 507 MET cc_start: 0.7802 (mmm) cc_final: 0.7601 (mmm) REVERT: B 568 ILE cc_start: 0.8816 (mt) cc_final: 0.7908 (tp) REVERT: B 645 MET cc_start: 0.8020 (mpp) cc_final: 0.7689 (mpp) REVERT: B 656 GLU cc_start: 0.8835 (tt0) cc_final: 0.8497 (tt0) REVERT: B 685 ASP cc_start: 0.8059 (t0) cc_final: 0.7741 (t70) REVERT: B 718 MET cc_start: 0.8406 (mtm) cc_final: 0.8082 (mtp) REVERT: B 724 ILE cc_start: 0.8516 (mm) cc_final: 0.8108 (tp) REVERT: C 23 THR cc_start: 0.8600 (m) cc_final: 0.8369 (p) REVERT: C 90 MET cc_start: 0.6309 (ptp) cc_final: 0.6024 (mtt) REVERT: C 202 MET cc_start: 0.9439 (mmm) cc_final: 0.9062 (mmp) outliers start: 2 outliers final: 1 residues processed: 270 average time/residue: 0.5743 time to fit residues: 229.1550 Evaluate side-chains 219 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15287 Z= 0.225 Angle : 0.587 26.209 20719 Z= 0.314 Chirality : 0.038 0.166 2270 Planarity : 0.005 0.096 2589 Dihedral : 10.260 73.898 2314 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 1784 helix: -0.02 (0.17), residues: 794 sheet: -0.71 (0.36), residues: 192 loop : -1.58 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 99 HIS 0.006 0.001 HIS B 605 PHE 0.031 0.002 PHE B 412 TYR 0.012 0.001 TYR A 334 ARG 0.026 0.001 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.836 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: A 97 THR cc_start: 0.8138 (p) cc_final: 0.7724 (p) REVERT: A 334 TYR cc_start: 0.7352 (m-80) cc_final: 0.6638 (m-80) REVERT: A 477 MET cc_start: 0.7967 (pmm) cc_final: 0.7729 (mpp) REVERT: A 485 MET cc_start: 0.8119 (mtp) cc_final: 0.7809 (mtt) REVERT: A 540 TYR cc_start: 0.7590 (m-80) cc_final: 0.7388 (m-80) REVERT: B 3 VAL cc_start: 0.6535 (t) cc_final: 0.5907 (t) REVERT: B 408 MET cc_start: 0.3147 (tpt) cc_final: 0.2940 (tpt) REVERT: B 568 ILE cc_start: 0.8885 (mt) cc_final: 0.7999 (tp) REVERT: B 690 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B 724 ILE cc_start: 0.8458 (mm) cc_final: 0.7945 (tp) REVERT: C 23 THR cc_start: 0.8614 (m) cc_final: 0.8384 (p) REVERT: C 164 MET cc_start: 0.8828 (ttp) cc_final: 0.8543 (ttm) REVERT: C 202 MET cc_start: 0.9581 (mmm) cc_final: 0.9154 (mmp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.5356 time to fit residues: 213.8652 Evaluate side-chains 210 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 154 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15287 Z= 0.189 Angle : 0.559 27.790 20719 Z= 0.294 Chirality : 0.037 0.164 2270 Planarity : 0.004 0.053 2589 Dihedral : 10.150 73.474 2314 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1784 helix: 0.52 (0.18), residues: 785 sheet: -0.59 (0.36), residues: 190 loop : -1.46 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 406 HIS 0.005 0.001 HIS B 562 PHE 0.027 0.002 PHE B 412 TYR 0.013 0.001 TYR B 30 ARG 0.004 0.000 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.0825 (tpt) cc_final: 0.0487 (tpt) REVERT: A 97 THR cc_start: 0.8066 (p) cc_final: 0.7834 (p) REVERT: A 334 TYR cc_start: 0.7739 (m-80) cc_final: 0.7359 (m-80) REVERT: A 477 MET cc_start: 0.7972 (pmm) cc_final: 0.7728 (mpp) REVERT: A 540 TYR cc_start: 0.7638 (m-80) cc_final: 0.7309 (m-80) REVERT: A 694 LEU cc_start: 0.8710 (mt) cc_final: 0.8282 (mp) REVERT: B 3 VAL cc_start: 0.6529 (t) cc_final: 0.6013 (t) REVERT: B 343 MET cc_start: 0.7791 (mmm) cc_final: 0.7442 (mmm) REVERT: B 568 ILE cc_start: 0.8947 (mt) cc_final: 0.8086 (tp) REVERT: B 690 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 718 MET cc_start: 0.8923 (mtp) cc_final: 0.7766 (mmm) REVERT: B 724 ILE cc_start: 0.8472 (mm) cc_final: 0.7972 (tp) REVERT: C 7 LEU cc_start: 0.8320 (tt) cc_final: 0.7995 (tt) REVERT: C 23 THR cc_start: 0.8629 (m) cc_final: 0.8415 (p) REVERT: C 90 MET cc_start: 0.6608 (ptp) cc_final: 0.5584 (ptp) REVERT: C 164 MET cc_start: 0.8870 (ttp) cc_final: 0.8566 (ttm) REVERT: C 202 MET cc_start: 0.9636 (mmm) cc_final: 0.9289 (mmp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.5610 time to fit residues: 211.5108 Evaluate side-chains 211 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 15287 Z= 0.329 Angle : 0.678 26.434 20719 Z= 0.368 Chirality : 0.039 0.166 2270 Planarity : 0.005 0.074 2589 Dihedral : 10.492 75.334 2314 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.11 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.19), residues: 1784 helix: -0.07 (0.17), residues: 789 sheet: -0.62 (0.37), residues: 196 loop : -1.67 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 99 HIS 0.010 0.002 HIS B 562 PHE 0.030 0.002 PHE B 730 TYR 0.022 0.002 TYR B 355 ARG 0.009 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.520 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: A 21 MET cc_start: 0.1450 (tpt) cc_final: 0.1095 (tpt) REVERT: A 211 MET cc_start: 0.4126 (ttt) cc_final: 0.3668 (ttt) REVERT: A 214 LEU cc_start: 0.8469 (mt) cc_final: 0.8205 (mt) REVERT: A 540 TYR cc_start: 0.7762 (m-80) cc_final: 0.7509 (m-80) REVERT: B 40 MET cc_start: 0.7637 (mtm) cc_final: 0.7431 (mtp) REVERT: B 343 MET cc_start: 0.7860 (mmm) cc_final: 0.7578 (mmm) REVERT: B 507 MET cc_start: 0.7832 (mmm) cc_final: 0.7501 (mmp) REVERT: B 646 MET cc_start: 0.7054 (tpt) cc_final: 0.6272 (ppp) REVERT: B 690 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 718 MET cc_start: 0.8872 (mtp) cc_final: 0.8640 (mtp) REVERT: B 724 ILE cc_start: 0.8151 (mm) cc_final: 0.7789 (tp) REVERT: C 42 ASN cc_start: 0.8939 (t0) cc_final: 0.8699 (t0) REVERT: C 164 MET cc_start: 0.8978 (ttp) cc_final: 0.8714 (ttm) REVERT: C 202 MET cc_start: 0.9257 (mmm) cc_final: 0.8922 (mmp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.5391 time to fit residues: 195.0372 Evaluate side-chains 200 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15287 Z= 0.269 Angle : 0.618 26.661 20719 Z= 0.334 Chirality : 0.039 0.172 2270 Planarity : 0.005 0.059 2589 Dihedral : 10.513 78.867 2314 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.19), residues: 1784 helix: -0.00 (0.17), residues: 802 sheet: -0.66 (0.36), residues: 202 loop : -1.77 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 619 HIS 0.006 0.002 HIS C 233 PHE 0.027 0.002 PHE B 730 TYR 0.019 0.002 TYR A 334 ARG 0.006 0.001 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.371 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: A 285 MET cc_start: 0.8248 (tmm) cc_final: 0.8040 (tmm) REVERT: A 540 TYR cc_start: 0.7716 (m-80) cc_final: 0.7462 (m-80) REVERT: B 343 MET cc_start: 0.8113 (mmm) cc_final: 0.7869 (mmm) REVERT: B 507 MET cc_start: 0.7890 (mmm) cc_final: 0.7449 (mmp) REVERT: B 646 MET cc_start: 0.7043 (tpt) cc_final: 0.6220 (ppp) REVERT: B 649 HIS cc_start: 0.7202 (t-90) cc_final: 0.6928 (t-90) REVERT: B 690 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 718 MET cc_start: 0.9076 (mtp) cc_final: 0.8704 (mtp) REVERT: B 724 ILE cc_start: 0.8553 (mm) cc_final: 0.8163 (tp) REVERT: C 7 LEU cc_start: 0.8823 (tt) cc_final: 0.8561 (tt) REVERT: C 11 MET cc_start: 0.7693 (mmm) cc_final: 0.7325 (mmt) REVERT: C 164 MET cc_start: 0.8906 (ttm) cc_final: 0.8355 (ttm) REVERT: C 202 MET cc_start: 0.9222 (mmm) cc_final: 0.8919 (mmm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.5355 time to fit residues: 188.1396 Evaluate side-chains 193 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 172 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15287 Z= 0.201 Angle : 0.589 27.610 20719 Z= 0.311 Chirality : 0.038 0.165 2270 Planarity : 0.004 0.062 2589 Dihedral : 10.511 80.813 2314 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.19), residues: 1784 helix: 0.39 (0.18), residues: 801 sheet: -0.50 (0.37), residues: 188 loop : -1.75 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 406 HIS 0.007 0.001 HIS B 562 PHE 0.025 0.001 PHE B 730 TYR 0.038 0.002 TYR B 82 ARG 0.015 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.212 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 21 MET cc_start: 0.1895 (tpt) cc_final: 0.1608 (tpt) REVERT: A 285 MET cc_start: 0.8269 (tmm) cc_final: 0.7975 (tmm) REVERT: A 540 TYR cc_start: 0.7681 (m-80) cc_final: 0.7446 (m-80) REVERT: B 279 LYS cc_start: 0.8070 (mttt) cc_final: 0.7593 (pttp) REVERT: B 507 MET cc_start: 0.7846 (mmm) cc_final: 0.7224 (mmp) REVERT: B 646 MET cc_start: 0.7081 (tpt) cc_final: 0.6335 (ppp) REVERT: B 649 HIS cc_start: 0.7190 (t-90) cc_final: 0.6952 (t70) REVERT: B 690 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 718 MET cc_start: 0.9141 (mtp) cc_final: 0.8690 (mtp) REVERT: B 724 ILE cc_start: 0.8614 (mm) cc_final: 0.8232 (tp) REVERT: C 7 LEU cc_start: 0.8848 (tt) cc_final: 0.8525 (tt) REVERT: C 202 MET cc_start: 0.9107 (mmm) cc_final: 0.8860 (mmm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.5628 time to fit residues: 198.6848 Evaluate side-chains 195 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.8012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15287 Z= 0.267 Angle : 0.637 26.894 20719 Z= 0.340 Chirality : 0.040 0.216 2270 Planarity : 0.005 0.067 2589 Dihedral : 10.683 83.504 2314 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 1784 helix: 0.13 (0.17), residues: 802 sheet: -0.76 (0.35), residues: 204 loop : -1.97 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 406 HIS 0.008 0.002 HIS B 562 PHE 0.026 0.002 PHE B 730 TYR 0.020 0.002 TYR B 82 ARG 0.006 0.001 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.179 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: A 21 MET cc_start: 0.3254 (tpt) cc_final: 0.2896 (tpt) REVERT: A 285 MET cc_start: 0.8323 (tmm) cc_final: 0.7927 (tmm) REVERT: A 543 LEU cc_start: 0.8348 (tp) cc_final: 0.7772 (tp) REVERT: B 279 LYS cc_start: 0.8081 (mttt) cc_final: 0.7511 (pttp) REVERT: B 356 MET cc_start: 0.7338 (ttm) cc_final: 0.7130 (ttm) REVERT: B 507 MET cc_start: 0.7980 (mmm) cc_final: 0.7277 (mmp) REVERT: B 645 MET cc_start: 0.8333 (mpp) cc_final: 0.8029 (mpp) REVERT: B 646 MET cc_start: 0.7063 (tpt) cc_final: 0.6250 (ppp) REVERT: B 690 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 718 MET cc_start: 0.9183 (mtp) cc_final: 0.8776 (mtp) REVERT: B 724 ILE cc_start: 0.8521 (mm) cc_final: 0.8088 (tp) REVERT: C 7 LEU cc_start: 0.8887 (tt) cc_final: 0.8555 (tt) REVERT: C 90 MET cc_start: 0.6922 (ptp) cc_final: 0.5919 (mtt) REVERT: C 202 MET cc_start: 0.9119 (mmm) cc_final: 0.8880 (mmm) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.5702 time to fit residues: 197.6941 Evaluate side-chains 193 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15287 Z= 0.178 Angle : 0.567 27.114 20719 Z= 0.298 Chirality : 0.038 0.172 2270 Planarity : 0.004 0.046 2589 Dihedral : 10.598 85.909 2314 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 1784 helix: 0.54 (0.18), residues: 795 sheet: -0.78 (0.35), residues: 201 loop : -1.86 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.006 0.001 HIS B 562 PHE 0.023 0.002 PHE B 150 TYR 0.016 0.001 TYR B 82 ARG 0.006 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.461 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: A 21 MET cc_start: 0.2750 (tpt) cc_final: 0.2217 (tpt) REVERT: A 285 MET cc_start: 0.8288 (tmm) cc_final: 0.7885 (tmm) REVERT: B 163 LEU cc_start: 0.9381 (tt) cc_final: 0.9076 (tt) REVERT: B 279 LYS cc_start: 0.8020 (mttt) cc_final: 0.7473 (pttp) REVERT: B 645 MET cc_start: 0.8314 (mpp) cc_final: 0.8094 (mpp) REVERT: B 646 MET cc_start: 0.6962 (tpt) cc_final: 0.6229 (ppp) REVERT: B 690 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8568 (tm-30) REVERT: B 718 MET cc_start: 0.9248 (mtp) cc_final: 0.8837 (mtp) REVERT: B 724 ILE cc_start: 0.8757 (mm) cc_final: 0.8276 (tp) REVERT: C 7 LEU cc_start: 0.8856 (tt) cc_final: 0.8580 (tt) REVERT: C 34 TYR cc_start: 0.7481 (t80) cc_final: 0.6952 (t80) REVERT: C 90 MET cc_start: 0.7125 (ptp) cc_final: 0.5978 (mtt) REVERT: C 202 MET cc_start: 0.9090 (mmm) cc_final: 0.8873 (mmm) REVERT: F 34 MET cc_start: 0.1033 (mpp) cc_final: 0.0696 (mpp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.5489 time to fit residues: 189.9135 Evaluate side-chains 189 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15287 Z= 0.184 Angle : 0.555 26.937 20719 Z= 0.292 Chirality : 0.037 0.170 2270 Planarity : 0.005 0.090 2589 Dihedral : 10.591 88.112 2314 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1784 helix: 0.58 (0.18), residues: 803 sheet: -0.63 (0.37), residues: 190 loop : -1.82 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 406 HIS 0.006 0.001 HIS B 605 PHE 0.021 0.001 PHE B 730 TYR 0.029 0.001 TYR A 130 ARG 0.010 0.000 ARG B 754 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.364 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: A 21 MET cc_start: 0.2764 (tpt) cc_final: 0.2324 (tpt) REVERT: A 285 MET cc_start: 0.8262 (tmm) cc_final: 0.7851 (tmm) REVERT: A 540 TYR cc_start: 0.7684 (m-80) cc_final: 0.7431 (m-80) REVERT: B 163 LEU cc_start: 0.9326 (tt) cc_final: 0.8997 (tt) REVERT: B 279 LYS cc_start: 0.8081 (mttt) cc_final: 0.7419 (pttp) REVERT: B 507 MET cc_start: 0.8062 (mmm) cc_final: 0.7242 (mmp) REVERT: B 645 MET cc_start: 0.8306 (mpp) cc_final: 0.8064 (mpp) REVERT: B 646 MET cc_start: 0.6914 (tpt) cc_final: 0.6157 (ppp) REVERT: B 690 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8590 (tm-30) REVERT: B 718 MET cc_start: 0.9256 (mtp) cc_final: 0.8831 (mtp) REVERT: B 724 ILE cc_start: 0.8565 (mm) cc_final: 0.8138 (tp) REVERT: C 7 LEU cc_start: 0.8887 (tt) cc_final: 0.8574 (tt) REVERT: C 47 MET cc_start: 0.8018 (tpp) cc_final: 0.7650 (tpp) REVERT: C 90 MET cc_start: 0.6850 (ptp) cc_final: 0.5915 (mtt) REVERT: C 202 MET cc_start: 0.9086 (mmm) cc_final: 0.8863 (mmm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.5297 time to fit residues: 187.2806 Evaluate side-chains 188 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 0.0050 chunk 142 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.107020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.086297 restraints weight = 181878.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.090532 restraints weight = 91956.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.093337 restraints weight = 55509.484| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15287 Z= 0.153 Angle : 0.536 26.813 20719 Z= 0.279 Chirality : 0.037 0.167 2270 Planarity : 0.004 0.099 2589 Dihedral : 10.556 90.012 2314 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1784 helix: 0.90 (0.18), residues: 793 sheet: -0.53 (0.38), residues: 187 loop : -1.67 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 537 HIS 0.005 0.001 HIS B 562 PHE 0.020 0.001 PHE B 730 TYR 0.012 0.001 TYR B 82 ARG 0.005 0.000 ARG A 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5787.83 seconds wall clock time: 103 minutes 47.66 seconds (6227.66 seconds total)