Starting phenix.real_space_refine on Wed Sep 25 14:12:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/09_2024/7pm7_13523.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/09_2024/7pm7_13523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/09_2024/7pm7_13523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/09_2024/7pm7_13523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/09_2024/7pm7_13523.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/09_2024/7pm7_13523.cif" } resolution = 3.5 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= 0.000 sd= 0.001 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 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1724 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6070 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 27, 'TRANS': 715} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.38, per 1000 atoms: 0.63 Number of scatterers: 10149 At special positions: 0 Unit cell: (107.06, 139.92, 147.34, 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 63 16.00 P 4 15.00 Mg 2 11.99 O 1894 8.00 N 1724 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 15 sheets defined 56.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.284A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 66 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.399A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.578A pdb=" N SER A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.781A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.147A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.895A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.967A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.672A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.597A pdb=" N PHE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.521A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.899A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.592A pdb=" N ILE A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.525A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.508A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.521A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.993A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.042A pdb=" N LYS A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 635 through 653 removed outlier: 4.090A pdb=" N ARG A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.804A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 720 removed outlier: 3.886A pdb=" N VAL A 720 " --> pdb=" O GLN A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.706A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.690A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.118A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.673A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.535A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.813A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.591A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.518A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.779A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.284A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.566A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 375 removed outlier: 3.501A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 16 removed outlier: 3.866A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.408A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.761A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.831A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.608A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 524 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1690 1.32 - 1.44: 2740 1.44 - 1.57: 5826 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10364 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.451 0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.74e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.67e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 ... (remaining 10359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13670 2.38 - 4.77: 289 4.77 - 7.15: 30 7.15 - 9.53: 7 9.53 - 11.91: 4 Bond angle restraints: 14000 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.79 11.91 1.80e+00 3.09e-01 4.38e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.80 -4.80 1.10e+00 8.26e-01 1.90e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.28 4.12 1.00e+00 1.00e+00 1.69e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 105.01 6.49 1.70e+00 3.46e-01 1.46e+01 ... (remaining 13995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 6083 32.71 - 65.42: 139 65.42 - 98.12: 28 98.12 - 130.83: 3 130.83 - 163.54: 1 Dihedral angle restraints: 6254 sinusoidal: 2572 harmonic: 3682 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.46 163.54 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 66.38 -126.38 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 176.15 123.85 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 6251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1011 0.041 - 0.083: 353 0.083 - 0.124: 130 0.124 - 0.165: 27 0.165 - 0.207: 9 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA PHE C 255 " pdb=" N PHE C 255 " pdb=" C PHE C 255 " pdb=" CB PHE C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET A 364 " pdb=" N MET A 364 " pdb=" C MET A 364 " pdb=" CB MET A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE C 124 " pdb=" N PHE C 124 " pdb=" C PHE C 124 " pdb=" CB PHE C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 1527 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.114 9.50e-02 1.11e+02 6.65e-02 2.44e+01 pdb=" NE ARG A 248 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 0.284 9.50e-02 1.11e+02 1.31e-01 2.06e+01 pdb=" NE ARG A 213 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 312 " -0.101 9.50e-02 1.11e+02 5.85e-02 1.85e+01 pdb=" NE ARG C 312 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.020 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 16 2.37 - 3.00: 5470 3.00 - 3.63: 15098 3.63 - 4.27: 22662 4.27 - 4.90: 38361 Nonbonded interactions: 81607 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.140 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.141 3.040 nonbonded pdb=" O PHE A 698 " pdb=" NH1 ARG A 701 " model vdw 2.154 3.120 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 2.220 2.170 ... (remaining 81602 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: 6.170 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.121 10364 Z= 0.272 Angle : 0.851 11.913 14000 Z= 0.500 Chirality : 0.050 0.207 1530 Planarity : 0.008 0.131 1785 Dihedral : 15.671 163.540 3874 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.09 % Allowed : 0.46 % Favored : 99.44 % Cbeta Deviations : 0.08 % 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: -1.31 (0.21), residues: 1231 helix: -1.57 (0.17), residues: 589 sheet: 0.64 (0.39), residues: 148 loop : -0.16 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP C 340 HIS 0.007 0.001 HIS C 371 PHE 0.032 0.002 PHE C 255 TYR 0.044 0.006 TYR A 113 ARG 0.083 0.011 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 242 LEU cc_start: 0.8896 (mt) cc_final: 0.8164 (mp) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.2433 time to fit residues: 50.8796 Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 191 ASN A 264 GLN A 354 HIS A 395 HIS A 462 GLN A 463 GLN C 12 ASN C 162 ASN C 173 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10364 Z= 0.202 Angle : 0.636 7.840 14000 Z= 0.332 Chirality : 0.044 0.282 1530 Planarity : 0.004 0.042 1785 Dihedral : 9.465 142.587 1404 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.74 % Allowed : 6.01 % Favored : 93.25 % 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: 0.97 (0.24), residues: 1231 helix: 0.77 (0.20), residues: 616 sheet: 0.94 (0.38), residues: 160 loop : 0.60 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.008 0.001 HIS C 275 PHE 0.024 0.002 PHE C 255 TYR 0.032 0.001 TYR A 102 ARG 0.006 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 MET cc_start: 0.8077 (mmp) cc_final: 0.7561 (mmp) REVERT: A 484 TRP cc_start: 0.5957 (m-10) cc_final: 0.5358 (m-10) outliers start: 8 outliers final: 4 residues processed: 109 average time/residue: 0.2223 time to fit residues: 36.7323 Evaluate side-chains 85 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 122 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN C 12 ASN C 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10364 Z= 0.154 Angle : 0.560 7.569 14000 Z= 0.285 Chirality : 0.041 0.177 1530 Planarity : 0.004 0.051 1785 Dihedral : 7.248 85.697 1403 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.39 % Allowed : 6.66 % Favored : 91.95 % 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: 1.75 (0.24), residues: 1231 helix: 1.55 (0.21), residues: 609 sheet: 1.24 (0.40), residues: 159 loop : 0.79 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.022 0.001 TYR A 102 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4136 (mtt) cc_final: 0.3461 (mmt) REVERT: A 478 MET cc_start: 0.7867 (mmp) cc_final: 0.7603 (mmp) REVERT: A 484 TRP cc_start: 0.5889 (m-10) cc_final: 0.5350 (m-10) REVERT: A 775 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: C 154 ASP cc_start: 0.7863 (t0) cc_final: 0.7369 (t70) outliers start: 15 outliers final: 6 residues processed: 104 average time/residue: 0.2271 time to fit residues: 34.0277 Evaluate side-chains 80 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 76 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10364 Z= 0.169 Angle : 0.561 7.235 14000 Z= 0.283 Chirality : 0.041 0.173 1530 Planarity : 0.004 0.052 1785 Dihedral : 6.763 74.571 1403 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.20 % Allowed : 8.33 % Favored : 90.47 % 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: 1.90 (0.24), residues: 1231 helix: 1.73 (0.21), residues: 605 sheet: 1.35 (0.40), residues: 159 loop : 0.76 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 PHE 0.017 0.001 PHE A 360 TYR 0.017 0.001 TYR A 102 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.3878 (mtt) cc_final: 0.3203 (mmt) REVERT: A 478 MET cc_start: 0.7833 (mmp) cc_final: 0.7157 (mmp) REVERT: A 484 TRP cc_start: 0.5931 (m-10) cc_final: 0.5153 (m-10) REVERT: A 515 MET cc_start: 0.8458 (tpt) cc_final: 0.8129 (tpt) REVERT: A 775 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8429 (mp10) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.2266 time to fit residues: 29.5436 Evaluate side-chains 74 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN A 775 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10364 Z= 0.247 Angle : 0.587 8.096 14000 Z= 0.296 Chirality : 0.042 0.176 1530 Planarity : 0.004 0.051 1785 Dihedral : 6.542 67.285 1403 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.39 % Allowed : 8.60 % Favored : 90.01 % 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: 1.90 (0.24), residues: 1231 helix: 1.75 (0.21), residues: 614 sheet: 1.35 (0.40), residues: 159 loop : 0.70 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS C 275 PHE 0.016 0.001 PHE C 255 TYR 0.015 0.001 TYR A 102 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9238 (ppt170) cc_final: 0.8893 (ppt170) REVERT: B 120 MET cc_start: 0.4064 (mtt) cc_final: 0.3335 (mmt) REVERT: A 775 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8269 (mp10) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.2030 time to fit residues: 25.8886 Evaluate side-chains 79 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 29 optimal weight: 0.0970 chunk 120 optimal weight: 0.0170 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 0.0670 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10364 Z= 0.136 Angle : 0.557 7.702 14000 Z= 0.275 Chirality : 0.041 0.174 1530 Planarity : 0.004 0.054 1785 Dihedral : 6.192 67.740 1403 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.02 % Allowed : 9.34 % Favored : 89.64 % 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: 2.04 (0.25), residues: 1231 helix: 1.90 (0.21), residues: 608 sheet: 1.47 (0.40), residues: 159 loop : 0.72 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.016 0.001 PHE A 360 TYR 0.015 0.001 TYR A 102 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7838 (mmt) REVERT: B 110 ARG cc_start: 0.9196 (ppt170) cc_final: 0.8855 (ppt170) REVERT: B 120 MET cc_start: 0.3882 (mtt) cc_final: 0.3179 (mmt) REVERT: A 515 MET cc_start: 0.8424 (tpt) cc_final: 0.8156 (tpt) REVERT: A 775 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: C 154 ASP cc_start: 0.7749 (t70) cc_final: 0.7318 (t70) outliers start: 11 outliers final: 5 residues processed: 86 average time/residue: 0.2188 time to fit residues: 27.6314 Evaluate side-chains 78 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.2980 chunk 68 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 418 HIS A 775 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10364 Z= 0.167 Angle : 0.561 8.259 14000 Z= 0.279 Chirality : 0.041 0.172 1530 Planarity : 0.004 0.053 1785 Dihedral : 6.050 67.627 1403 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.93 % Allowed : 9.81 % Favored : 89.27 % 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: 2.12 (0.25), residues: 1231 helix: 1.98 (0.22), residues: 608 sheet: 1.53 (0.41), residues: 159 loop : 0.72 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 484 HIS 0.010 0.001 HIS A 418 PHE 0.016 0.001 PHE A 360 TYR 0.014 0.001 TYR A 102 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9220 (ppt170) cc_final: 0.8882 (ppt170) REVERT: B 120 MET cc_start: 0.4561 (mtt) cc_final: 0.3768 (mmt) REVERT: A 515 MET cc_start: 0.8530 (tpt) cc_final: 0.8264 (tpt) REVERT: C 154 ASP cc_start: 0.7738 (t70) cc_final: 0.7297 (t70) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.2213 time to fit residues: 27.7981 Evaluate side-chains 78 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 0.0170 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10364 Z= 0.185 Angle : 0.568 8.217 14000 Z= 0.283 Chirality : 0.041 0.176 1530 Planarity : 0.004 0.053 1785 Dihedral : 5.985 67.203 1403 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.11 % Allowed : 10.27 % Favored : 88.62 % 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: 2.12 (0.25), residues: 1231 helix: 1.95 (0.21), residues: 608 sheet: 1.58 (0.41), residues: 159 loop : 0.76 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 484 HIS 0.005 0.001 HIS A 354 PHE 0.022 0.001 PHE A 470 TYR 0.019 0.001 TYR A 711 ARG 0.006 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7776 (mmm) REVERT: B 110 ARG cc_start: 0.9218 (ppt170) cc_final: 0.8910 (ppt170) REVERT: B 120 MET cc_start: 0.4598 (mtt) cc_final: 0.3818 (mmt) REVERT: A 515 MET cc_start: 0.8541 (tpt) cc_final: 0.8183 (tpt) REVERT: A 775 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: C 154 ASP cc_start: 0.7707 (t70) cc_final: 0.7270 (t70) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2152 time to fit residues: 25.7596 Evaluate side-chains 78 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10364 Z= 0.180 Angle : 0.573 7.797 14000 Z= 0.284 Chirality : 0.041 0.175 1530 Planarity : 0.004 0.056 1785 Dihedral : 5.840 67.074 1403 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.02 % Allowed : 10.08 % Favored : 88.90 % 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: 2.15 (0.25), residues: 1231 helix: 2.00 (0.21), residues: 608 sheet: 1.56 (0.41), residues: 159 loop : 0.74 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.016 0.001 PHE A 360 TYR 0.014 0.001 TYR A 102 ARG 0.007 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9218 (ppt170) cc_final: 0.8893 (ppt170) REVERT: B 120 MET cc_start: 0.4775 (mtt) cc_final: 0.4222 (tpt) REVERT: A 515 MET cc_start: 0.8473 (tpt) cc_final: 0.8142 (tpt) REVERT: A 775 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: C 154 ASP cc_start: 0.7679 (t70) cc_final: 0.7209 (t70) REVERT: C 205 GLU cc_start: 0.7443 (pt0) cc_final: 0.7147 (pt0) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.2170 time to fit residues: 26.0686 Evaluate side-chains 79 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.0726 > 50: distance: 55 - 140: 25.836 distance: 58 - 137: 16.341 distance: 68 - 121: 7.379 distance: 71 - 118: 17.184 distance: 90 - 95: 8.394 distance: 95 - 96: 20.487 distance: 96 - 97: 12.332 distance: 96 - 99: 13.381 distance: 97 - 98: 33.145 distance: 97 - 105: 9.837 distance: 99 - 100: 20.203 distance: 100 - 101: 20.241 distance: 100 - 102: 25.703 distance: 101 - 103: 9.392 distance: 102 - 104: 9.721 distance: 103 - 104: 25.875 distance: 105 - 106: 6.261 distance: 106 - 107: 20.048 distance: 106 - 109: 21.904 distance: 107 - 108: 4.094 distance: 107 - 110: 5.567 distance: 110 - 111: 14.429 distance: 111 - 112: 22.128 distance: 111 - 114: 19.582 distance: 112 - 118: 30.595 distance: 114 - 115: 16.275 distance: 114 - 116: 15.564 distance: 115 - 117: 20.546 distance: 118 - 119: 14.069 distance: 119 - 120: 9.294 distance: 119 - 122: 15.492 distance: 120 - 121: 8.682 distance: 120 - 126: 5.965 distance: 122 - 123: 13.541 distance: 123 - 124: 7.294 distance: 124 - 125: 15.582 distance: 126 - 127: 13.415 distance: 127 - 128: 6.602 distance: 127 - 130: 11.915 distance: 128 - 129: 9.585 distance: 128 - 137: 17.117 distance: 130 - 131: 11.481 distance: 131 - 132: 14.782 distance: 132 - 133: 8.532 distance: 133 - 134: 9.526 distance: 134 - 135: 10.880 distance: 134 - 136: 26.169 distance: 137 - 138: 22.603 distance: 138 - 139: 23.230 distance: 138 - 141: 40.394 distance: 139 - 140: 4.381 distance: 139 - 145: 4.992 distance: 141 - 142: 40.588 distance: 142 - 143: 33.664 distance: 142 - 144: 23.864 distance: 145 - 146: 25.601 distance: 146 - 147: 5.026 distance: 146 - 149: 34.648 distance: 147 - 148: 15.368 distance: 149 - 150: 3.258 distance: 150 - 151: 30.534 distance: 150 - 152: 17.036 distance: 153 - 154: 29.337 distance: 154 - 155: 34.327 distance: 154 - 157: 22.718 distance: 155 - 156: 22.062 distance: 155 - 161: 23.034 distance: 157 - 158: 18.091 distance: 158 - 159: 42.519 distance: 158 - 160: 7.879 distance: 161 - 162: 39.302 distance: 162 - 163: 18.328 distance: 162 - 165: 30.250 distance: 163 - 164: 29.299 distance: 163 - 166: 4.670 distance: 164 - 184: 28.998 distance: 166 - 167: 17.535 distance: 167 - 168: 9.587 distance: 168 - 169: 23.782 distance: 168 - 170: 20.799 distance: 169 - 191: 17.420