Starting phenix.real_space_refine on Tue Jun 24 20:22:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nk1_12428/06_2025/7nk1_12428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nk1_12428/06_2025/7nk1_12428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nk1_12428/06_2025/7nk1_12428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nk1_12428/06_2025/7nk1_12428.map" model { file = "/net/cci-nas-00/data/ceres_data/7nk1_12428/06_2025/7nk1_12428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nk1_12428/06_2025/7nk1_12428.cif" } resolution = 4.22 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= 0.003 sd= 0.037 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 9289 2.51 5 N 2595 2.21 5 O 2866 1.98 5 H 13868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28747 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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 698 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 3 Time building chain proxies: 14.13, per 1000 atoms: 0.49 Number of scatterers: 28747 At special positions: 0 Unit cell: (97.2, 103.68, 158.76, 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 2866 8.00 N 2595 7.00 C 9289 6.00 H 13868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.08 Conformation dependent library (CDL) restraints added in 2.4 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 17 sheets defined 50.0% alpha, 13.8% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 14.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.140A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.005A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.691A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.793A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.431A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.947A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.637A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.635A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.972A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.732A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.778A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.529A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.827A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.587A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.508A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.511A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.616A 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: 4.331A 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: 3.892A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.107A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.237A 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: 3.523A 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: 3.659A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.302A 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 60 through 64 removed outlier: 3.504A pdb=" N ARG F 64 " --> pdb=" O ASP F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N HIS A 144 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.835A 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: 3.816A 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: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.690A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.717A 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: 6.035A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.174A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.345A 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: 3.515A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.634A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.810A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.522A pdb=" N LYS B 653 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.617A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.973A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.144A pdb=" N GLY F 10 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP F 96 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY F 35 " --> pdb=" O TRP F 96 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 1974 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: 12.03 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13841 1.03 - 1.23: 147 1.23 - 1.43: 6277 1.43 - 1.62: 8647 1.62 - 1.82: 183 Bond restraints: 29095 Sorted by residual: bond pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 1.510 1.472 0.039 1.20e-02 6.94e+03 1.03e+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 9.84e+00 bond pdb=" CD ARG F 66 " pdb=" NE ARG F 66 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.40e-02 5.10e+03 9.60e+00 bond pdb=" CD ARG F 45 " pdb=" NE ARG F 45 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.40e-02 5.10e+03 8.21e+00 bond pdb=" N PRO F 14 " pdb=" CA PRO F 14 " ideal model delta sigma weight residual 1.467 1.432 0.035 1.21e-02 6.83e+03 8.15e+00 ... (remaining 29090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 52225 5.65 - 11.29: 5 11.29 - 16.94: 0 16.94 - 22.59: 1 22.59 - 28.23: 5 Bond angle restraints: 52236 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 79.77 28.23 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 80.27 27.73 3.00e+00 1.11e-01 8.54e+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 81.82 27.18 3.00e+00 1.11e-01 8.21e+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 82.46 26.54 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 111.90 138.68 -26.78 3.20e+00 9.77e-02 7.00e+01 ... (remaining 52231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12542 17.94 - 35.88: 861 35.88 - 53.81: 253 53.81 - 71.75: 89 71.75 - 89.69: 16 Dihedral angle restraints: 13761 sinusoidal: 7724 harmonic: 6037 Sorted by residual: dihedral pdb=" CA TYR A 161 " pdb=" C TYR A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASP B 729 " pdb=" C ASP B 729 " pdb=" N PHE B 730 " pdb=" CA PHE B 730 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU B 731 " pdb=" C GLU B 731 " pdb=" N SER B 732 " pdb=" CA SER B 732 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 13758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2026 0.067 - 0.134: 214 0.134 - 0.201: 22 0.201 - 0.268: 2 0.268 - 0.335: 1 Chirality restraints: 2265 Sorted by residual: chirality pdb=" CA ASN F 76 " pdb=" N ASN F 76 " pdb=" C ASN F 76 " pdb=" CB ASN F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" C PRO F 41 " pdb=" CB PRO F 41 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASN F 84 " pdb=" N ASN F 84 " pdb=" C ASN F 84 " pdb=" CB ASN F 84 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2262 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 96 " -0.132 2.00e-02 2.50e+03 6.92e-02 1.20e+02 pdb=" CG TRP F 96 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP F 96 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP F 96 " 0.088 2.00e-02 2.50e+03 pdb=" NE1 TRP F 96 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP F 96 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP F 96 " 0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 96 " -0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 96 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP F 96 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " 0.111 2.00e-02 2.50e+03 6.23e-02 7.77e+01 pdb=" CG TYR F 37 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 108 " -0.054 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP F 108 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP F 108 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP F 108 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP F 108 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP F 108 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 108 " 0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 108 " -0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 108 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 108 " -0.039 2.00e-02 2.50e+03 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1256 2.17 - 2.78: 56190 2.78 - 3.39: 80855 3.39 - 3.99: 105792 3.99 - 4.60: 165058 Nonbonded interactions: 409151 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU A 153 " pdb=" H GLU A 153 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASP A 478 " pdb=" HE2 HIS A 510 " model vdw 1.595 2.450 nonbonded pdb=" OD1 ASP B 619 " pdb=" H TYR B 620 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.620 2.450 ... (remaining 409146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.550 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 75.790 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2043 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 0.044 15228 Z= 0.223 Angle : 0.691 26.779 20645 Z= 0.401 Chirality : 0.043 0.335 2265 Planarity : 0.005 0.076 2579 Dihedral : 14.324 89.689 5954 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.19 % Allowed : 0.44 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1775 helix: 0.46 (0.19), residues: 786 sheet: -0.79 (0.38), residues: 176 loop : -1.29 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.004 TRP F 96 HIS 0.003 0.001 HIS A 41 PHE 0.048 0.002 PHE A 446 TYR 0.111 0.002 TYR F 37 ARG 0.016 0.001 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.15070 ( 727) hydrogen bonds : angle 5.96927 ( 1994) SS BOND : bond 0.02507 ( 1) SS BOND : angle 5.06722 ( 2) covalent geometry : bond 0.00402 (15227) covalent geometry : angle 0.68913 (20643) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 334 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 2.027 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: A 561 MET cc_start: -0.1278 (tmm) cc_final: -0.1729 (tmm) REVERT: B 290 MET cc_start: 0.4741 (tpt) cc_final: 0.2823 (tpp) REVERT: B 408 MET cc_start: 0.3890 (tpt) cc_final: 0.3435 (tpt) REVERT: B 611 LEU cc_start: 0.3481 (tp) cc_final: 0.3114 (tt) REVERT: C 87 ASP cc_start: 0.2215 (p0) cc_final: 0.1817 (m-30) outliers start: 3 outliers final: 1 residues processed: 334 average time/residue: 0.7243 time to fit residues: 339.1474 Evaluate side-chains 222 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.4980 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN B 312 ASN B 425 ASN B 456 HIS B 676 ASN B 756 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5431 r_free = 0.5431 target = 0.267756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.247945 restraints weight = 107671.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.254194 restraints weight = 55443.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.257862 restraints weight = 31428.603| |-----------------------------------------------------------------------------| r_work (final): 0.5325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3000 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15228 Z= 0.147 Angle : 0.600 27.322 20645 Z= 0.317 Chirality : 0.039 0.166 2265 Planarity : 0.005 0.078 2579 Dihedral : 10.125 73.236 2304 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.64 (0.19), residues: 1775 helix: 0.42 (0.19), residues: 784 sheet: -0.75 (0.37), residues: 196 loop : -1.13 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 96 HIS 0.007 0.001 HIS C 134 PHE 0.020 0.002 PHE A 46 TYR 0.017 0.001 TYR C 111 ARG 0.007 0.001 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 727) hydrogen bonds : angle 5.06929 ( 1994) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.99354 ( 2) covalent geometry : bond 0.00318 (15227) covalent geometry : angle 0.60035 (20643) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 245 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 ASP cc_start: 0.4277 (m-30) cc_final: 0.4012 (m-30) REVERT: B 141 THR cc_start: 0.6082 (m) cc_final: 0.5797 (m) REVERT: B 290 MET cc_start: 0.5059 (tpt) cc_final: 0.4488 (tpt) REVERT: C 87 ASP cc_start: 0.3797 (p0) cc_final: 0.2798 (m-30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.6835 time to fit residues: 239.3965 Evaluate side-chains 201 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 24 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 50.0000 chunk 33 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN A 703 ASN B 65 GLN B 99 HIS B 134 ASN B 312 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5308 r_free = 0.5308 target = 0.251003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.227496 restraints weight = 107568.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.233868 restraints weight = 57987.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.238450 restraints weight = 35334.616| |-----------------------------------------------------------------------------| r_work (final): 0.5151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3757 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 15228 Z= 0.278 Angle : 0.817 25.270 20645 Z= 0.441 Chirality : 0.044 0.272 2265 Planarity : 0.007 0.068 2579 Dihedral : 10.589 73.164 2304 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.19 % Allowed : 3.60 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.50 (0.18), residues: 1775 helix: -0.53 (0.17), residues: 787 sheet: -0.58 (0.38), residues: 193 loop : -1.50 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 580 HIS 0.006 0.002 HIS C 110 PHE 0.039 0.003 PHE B 466 TYR 0.035 0.003 TYR B 559 ARG 0.016 0.001 ARG B 623 Details of bonding type rmsd hydrogen bonds : bond 0.06016 ( 727) hydrogen bonds : angle 5.64038 ( 1994) SS BOND : bond 0.00512 ( 1) SS BOND : angle 0.80418 ( 2) covalent geometry : bond 0.00612 (15227) covalent geometry : angle 0.81742 (20643) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 256 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 1.972 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 79 ILE cc_start: 0.7962 (mm) cc_final: 0.7404 (mt) REVERT: A 581 MET cc_start: 0.4178 (mtp) cc_final: 0.3781 (mtt) REVERT: A 699 TRP cc_start: 0.6775 (t-100) cc_final: 0.6506 (t-100) REVERT: B 141 THR cc_start: 0.6118 (m) cc_final: 0.5461 (m) REVERT: B 290 MET cc_start: 0.5143 (tpt) cc_final: 0.4904 (tpt) REVERT: C 8 ARG cc_start: 0.6661 (ttp-170) cc_final: 0.6070 (tmt-80) REVERT: C 87 ASP cc_start: 0.4256 (p0) cc_final: 0.3095 (m-30) outliers start: 3 outliers final: 2 residues processed: 256 average time/residue: 0.7098 time to fit residues: 254.5346 Evaluate side-chains 221 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 165 optimal weight: 9.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN B 335 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 455 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 134 HIS ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.254253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.232121 restraints weight = 108455.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.238215 restraints weight = 57844.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.242627 restraints weight = 35160.124| |-----------------------------------------------------------------------------| r_work (final): 0.5191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3623 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15228 Z= 0.143 Angle : 0.604 27.983 20645 Z= 0.319 Chirality : 0.038 0.163 2265 Planarity : 0.005 0.078 2579 Dihedral : 10.327 75.218 2304 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.19), residues: 1775 helix: 0.01 (0.18), residues: 787 sheet: -0.55 (0.37), residues: 201 loop : -1.34 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 49 HIS 0.010 0.001 HIS A 144 PHE 0.017 0.002 PHE B 254 TYR 0.026 0.002 TYR B 30 ARG 0.006 0.001 ARG A 663 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 727) hydrogen bonds : angle 5.12695 ( 1994) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.41260 ( 2) covalent geometry : bond 0.00314 (15227) covalent geometry : angle 0.60385 (20643) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 239 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: -0.3326 (mmp) cc_final: -0.3548 (mmp) REVERT: A 477 MET cc_start: 0.6817 (mpp) cc_final: 0.6156 (mpp) REVERT: A 699 TRP cc_start: 0.6660 (t-100) cc_final: 0.6320 (t-100) REVERT: C 53 MET cc_start: 0.3657 (mmt) cc_final: 0.3417 (mmt) REVERT: C 87 ASP cc_start: 0.4209 (p0) cc_final: 0.3530 (m-30) REVERT: C 202 MET cc_start: 0.7098 (mmm) cc_final: 0.6743 (mmm) REVERT: C 211 LEU cc_start: 0.8158 (mt) cc_final: 0.7121 (mt) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.7580 time to fit residues: 258.7633 Evaluate side-chains 214 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 170 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 335 ASN B 367 GLN B 425 ASN B 476 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN F 5 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.252125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.229251 restraints weight = 108300.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.235722 restraints weight = 57660.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.240117 restraints weight = 34635.776| |-----------------------------------------------------------------------------| r_work (final): 0.5174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3694 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15228 Z= 0.136 Angle : 0.577 27.246 20645 Z= 0.304 Chirality : 0.038 0.163 2265 Planarity : 0.005 0.088 2579 Dihedral : 10.329 78.089 2304 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.06 % Allowed : 1.58 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.81 (0.19), residues: 1775 helix: 0.21 (0.18), residues: 794 sheet: -0.55 (0.37), residues: 199 loop : -1.26 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 580 HIS 0.003 0.001 HIS B 634 PHE 0.014 0.001 PHE A 446 TYR 0.020 0.002 TYR B 620 ARG 0.009 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 727) hydrogen bonds : angle 4.94194 ( 1994) SS BOND : bond 0.00704 ( 1) SS BOND : angle 0.81724 ( 2) covalent geometry : bond 0.00297 (15227) covalent geometry : angle 0.57744 (20643) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: -0.3297 (mmp) cc_final: -0.3518 (mmp) REVERT: A 460 MET cc_start: 0.3718 (ttm) cc_final: 0.3271 (ttm) REVERT: A 477 MET cc_start: 0.6837 (mpp) cc_final: 0.6206 (mpp) REVERT: B 372 MET cc_start: 0.3787 (ttm) cc_final: 0.3445 (ttm) REVERT: B 408 MET cc_start: 0.3413 (tpt) cc_final: 0.3198 (tpp) REVERT: C 53 MET cc_start: 0.3767 (mmt) cc_final: 0.3517 (mmt) REVERT: C 87 ASP cc_start: 0.4513 (p0) cc_final: 0.3825 (m-30) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.8154 time to fit residues: 277.2077 Evaluate side-chains 215 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 392 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 425 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5321 r_free = 0.5321 target = 0.251719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.229111 restraints weight = 107933.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.235159 restraints weight = 58105.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.239536 restraints weight = 35586.482| |-----------------------------------------------------------------------------| r_work (final): 0.5169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3733 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15228 Z= 0.135 Angle : 0.576 26.323 20645 Z= 0.303 Chirality : 0.038 0.160 2265 Planarity : 0.005 0.080 2579 Dihedral : 10.358 81.175 2304 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1775 helix: 0.31 (0.18), residues: 788 sheet: -0.60 (0.37), residues: 193 loop : -1.22 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 580 HIS 0.004 0.001 HIS A 144 PHE 0.017 0.002 PHE A 503 TYR 0.020 0.001 TYR B 620 ARG 0.008 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 727) hydrogen bonds : angle 4.95716 ( 1994) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.88541 ( 2) covalent geometry : bond 0.00299 (15227) covalent geometry : angle 0.57573 (20643) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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 239 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: -0.3258 (mmp) cc_final: -0.3497 (mmp) REVERT: A 477 MET cc_start: 0.6840 (mpp) cc_final: 0.5879 (mpp) REVERT: B 141 THR cc_start: 0.5504 (m) cc_final: 0.5270 (m) REVERT: B 372 MET cc_start: 0.3382 (ttm) cc_final: 0.3103 (ttm) REVERT: B 616 MET cc_start: 0.1468 (mtp) cc_final: 0.1057 (mtp) REVERT: B 655 MET cc_start: 0.2050 (mmm) cc_final: 0.1814 (mmt) REVERT: C 53 MET cc_start: 0.3806 (mmt) cc_final: 0.3447 (mmt) REVERT: C 87 ASP cc_start: 0.4506 (p0) cc_final: 0.3853 (m-30) REVERT: C 229 ILE cc_start: 0.8488 (mm) cc_final: 0.8194 (mm) REVERT: F 82 MET cc_start: 0.5881 (ptp) cc_final: 0.5158 (ptp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.6871 time to fit residues: 233.9698 Evaluate side-chains 218 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 74 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN B 425 ASN B 442 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS C 73 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5249 r_free = 0.5249 target = 0.242811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.216458 restraints weight = 112269.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.222756 restraints weight = 62957.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.227215 restraints weight = 40078.014| |-----------------------------------------------------------------------------| r_work (final): 0.5060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4158 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 15228 Z= 0.241 Angle : 0.751 28.019 20645 Z= 0.400 Chirality : 0.042 0.230 2265 Planarity : 0.006 0.079 2579 Dihedral : 10.842 87.617 2304 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.06 % Allowed : 1.83 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.53 (0.18), residues: 1775 helix: -0.43 (0.17), residues: 796 sheet: -0.54 (0.40), residues: 174 loop : -1.68 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 580 HIS 0.008 0.001 HIS C 233 PHE 0.043 0.003 PHE B 496 TYR 0.027 0.002 TYR B 30 ARG 0.016 0.001 ARG B 623 Details of bonding type rmsd hydrogen bonds : bond 0.05381 ( 727) hydrogen bonds : angle 5.49644 ( 1994) SS BOND : bond 0.00810 ( 1) SS BOND : angle 0.65191 ( 2) covalent geometry : bond 0.00535 (15227) covalent geometry : angle 0.75100 (20643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.4521 (mmm) cc_final: 0.4166 (tpt) REVERT: A 360 MET cc_start: 0.1884 (ttt) cc_final: 0.1263 (ttt) REVERT: A 441 MET cc_start: 0.7703 (tmm) cc_final: 0.6205 (tmm) REVERT: A 477 MET cc_start: 0.6894 (mpp) cc_final: 0.6262 (mpp) REVERT: A 523 MET cc_start: -0.2064 (mpp) cc_final: -0.2438 (mpp) REVERT: B 141 THR cc_start: 0.5767 (m) cc_final: 0.5523 (m) REVERT: B 302 ILE cc_start: 0.5173 (mt) cc_final: 0.4921 (mt) REVERT: B 372 MET cc_start: 0.3864 (ttm) cc_final: 0.3525 (ttm) REVERT: B 655 MET cc_start: 0.2156 (mmm) cc_final: 0.1804 (mmt) REVERT: B 700 PHE cc_start: 0.8348 (m-80) cc_final: 0.7964 (m-80) REVERT: C 53 MET cc_start: 0.4537 (mmt) cc_final: 0.4191 (mmt) REVERT: C 87 ASP cc_start: 0.4691 (p0) cc_final: 0.4005 (m-30) outliers start: 1 outliers final: 1 residues processed: 235 average time/residue: 0.7351 time to fit residues: 240.7695 Evaluate side-chains 215 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN B 65 GLN B 335 ASN B 425 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN C 73 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.246057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.220782 restraints weight = 111622.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.227115 restraints weight = 62730.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.231794 restraints weight = 39467.295| |-----------------------------------------------------------------------------| r_work (final): 0.5100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4003 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15228 Z= 0.139 Angle : 0.608 27.031 20645 Z= 0.319 Chirality : 0.038 0.167 2265 Planarity : 0.005 0.085 2579 Dihedral : 10.645 88.404 2304 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.14 (0.19), residues: 1775 helix: 0.01 (0.18), residues: 794 sheet: -0.60 (0.39), residues: 180 loop : -1.53 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 580 HIS 0.004 0.001 HIS B 634 PHE 0.019 0.002 PHE B 318 TYR 0.031 0.002 TYR B 30 ARG 0.027 0.001 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 727) hydrogen bonds : angle 5.10724 ( 1994) SS BOND : bond 0.00132 ( 1) SS BOND : angle 1.19270 ( 2) covalent geometry : bond 0.00313 (15227) covalent geometry : angle 0.60791 (20643) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.082 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: A 86 MET cc_start: 0.4514 (mmm) cc_final: 0.4181 (tpt) REVERT: A 182 MET cc_start: -0.3425 (mmp) cc_final: -0.3631 (mmp) REVERT: A 360 MET cc_start: 0.1938 (ttt) cc_final: 0.1377 (ttt) REVERT: A 523 MET cc_start: -0.2137 (mpp) cc_final: -0.2490 (mpp) REVERT: B 141 THR cc_start: 0.5647 (m) cc_final: 0.5285 (m) REVERT: B 302 ILE cc_start: 0.4865 (mt) cc_final: 0.4604 (mt) REVERT: B 372 MET cc_start: 0.3754 (ttm) cc_final: 0.3452 (ttm) REVERT: B 623 ARG cc_start: 0.7285 (mtt180) cc_final: 0.6168 (mtt-85) REVERT: B 655 MET cc_start: 0.2135 (mmm) cc_final: 0.1753 (mmt) REVERT: B 700 PHE cc_start: 0.8078 (m-80) cc_final: 0.7688 (m-80) REVERT: C 87 ASP cc_start: 0.4160 (p0) cc_final: 0.3632 (m-30) REVERT: F 36 TRP cc_start: 0.2625 (m100) cc_final: 0.2167 (m100) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.7018 time to fit residues: 226.0135 Evaluate side-chains 206 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.579 > 50: distance: 10 - 15: 28.717 distance: 15 - 16: 45.970 distance: 15 - 24: 15.791 distance: 16 - 17: 24.930 distance: 16 - 19: 6.035 distance: 16 - 25: 22.990 distance: 17 - 30: 40.556 distance: 19 - 20: 29.938 distance: 19 - 26: 33.367 distance: 19 - 27: 27.707 distance: 20 - 21: 33.724 distance: 20 - 28: 18.060 distance: 20 - 29: 22.082 distance: 21 - 22: 23.565 distance: 21 - 23: 18.239 distance: 30 - 31: 19.864 distance: 30 - 38: 41.173 distance: 31 - 32: 33.707 distance: 31 - 34: 21.498 distance: 31 - 39: 33.890 distance: 32 - 42: 40.376 distance: 34 - 35: 18.109 distance: 34 - 40: 20.063 distance: 34 - 41: 17.043 distance: 35 - 36: 39.813 distance: 35 - 37: 27.833 distance: 42 - 49: 3.084 distance: 43 - 44: 39.712 distance: 43 - 46: 22.758 distance: 44 - 45: 37.533 distance: 44 - 58: 40.025 distance: 46 - 47: 30.630 distance: 46 - 48: 25.519 distance: 46 - 51: 7.326 distance: 47 - 52: 18.228 distance: 47 - 53: 9.085 distance: 47 - 54: 9.200 distance: 48 - 55: 21.199 distance: 48 - 56: 7.561 distance: 48 - 57: 6.343 distance: 58 - 59: 43.397 distance: 58 - 63: 20.193 distance: 59 - 60: 34.305 distance: 59 - 62: 54.117 distance: 59 - 64: 39.207 distance: 60 - 61: 42.828 distance: 60 - 68: 42.283 distance: 61 - 116: 32.831 distance: 62 - 65: 4.071 distance: 62 - 66: 26.530 distance: 62 - 67: 20.710 distance: 68 - 69: 41.392 distance: 68 - 74: 9.165 distance: 69 - 70: 14.483 distance: 69 - 72: 36.102 distance: 69 - 75: 18.813 distance: 70 - 71: 20.886 distance: 70 - 82: 28.180 distance: 71 - 133: 49.245 distance: 72 - 73: 35.997 distance: 72 - 76: 29.478 distance: 72 - 77: 27.968 distance: 73 - 74: 12.685 distance: 73 - 78: 41.732 distance: 73 - 79: 33.890 distance: 74 - 80: 39.477 distance: 74 - 81: 5.681 distance: 82 - 83: 26.436 distance: 82 - 90: 11.717 distance: 83 - 84: 11.298 distance: 83 - 86: 6.839 distance: 83 - 91: 19.614 distance: 84 - 85: 27.851 distance: 84 - 101: 11.177 distance: 85 - 152: 55.118 distance: 86 - 87: 5.424 distance: 86 - 88: 10.746 distance: 86 - 92: 15.307 distance: 87 - 89: 18.574 distance: 87 - 93: 12.656 distance: 87 - 94: 15.524 distance: 88 - 95: 19.835 distance: 88 - 96: 10.284 distance: 88 - 97: 9.837 distance: 89 - 98: 5.139 distance: 89 - 100: 6.517 distance: 101 - 102: 11.860 distance: 101 - 110: 31.292 distance: 102 - 103: 27.517 distance: 102 - 105: 18.100 distance: 102 - 111: 22.801 distance: 103 - 104: 7.781 distance: 103 - 116: 30.690 distance: 104 - 162: 32.196 distance: 105 - 106: 26.678 distance: 105 - 112: 16.586 distance: 105 - 113: 11.635 distance: 106 - 107: 9.969 distance: 106 - 114: 17.365 distance: 106 - 115: 14.409 distance: 107 - 108: 12.870 distance: 107 - 109: 23.062 distance: 116 - 117: 14.502 distance: 116 - 126: 17.176 distance: 117 - 118: 26.583 distance: 117 - 120: 7.250 distance: 117 - 127: 3.565 distance: 118 - 119: 13.173 distance: 118 - 133: 13.738 distance: 119 - 173: 18.397 distance: 120 - 121: 18.358 distance: 120 - 128: 7.900 distance: 120 - 129: 11.137 distance: 121 - 122: 23.365 distance: 121 - 123: 19.312 distance: 122 - 124: 15.312 distance: 123 - 125: 18.607 distance: 123 - 130: 12.703 distance: 124 - 125: 14.817 distance: 124 - 131: 17.383 distance: 125 - 132: 11.821 distance: 133 - 134: 21.665 distance: 133 - 141: 15.076 distance: 134 - 135: 30.861 distance: 134 - 137: 20.523 distance: 134 - 142: 18.084 distance: 135 - 136: 12.291 distance: 135 - 152: 17.770 distance: 136 - 190: 37.534 distance: 137 - 138: 26.381 distance: 137 - 139: 14.127 distance: 137 - 143: 12.050 distance: 138 - 140: 16.383 distance: 138 - 144: 17.031 distance: 138 - 145: 19.488 distance: 139 - 146: 4.486 distance: 139 - 147: 9.760 distance: 139 - 148: 23.509 distance: 140 - 149: 8.516 distance: 140 - 150: 8.069 distance: 140 - 151: 6.876 distance: 152 - 153: 16.731 distance: 152 - 157: 51.209 distance: 153 - 154: 10.700 distance: 153 - 156: 22.284 distance: 153 - 158: 3.066 distance: 154 - 155: 3.742 distance: 154 - 162: 23.767 distance: 155 - 210: 26.154 distance: 156 - 159: 12.989 distance: 156 - 160: 14.603 distance: 156 - 161: 13.576