Starting phenix.real_space_refine on Sat Jun 21 01:59:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn7_19389/06_2025/8rn7_19389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn7_19389/06_2025/8rn7_19389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn7_19389/06_2025/8rn7_19389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn7_19389/06_2025/8rn7_19389.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn7_19389/06_2025/8rn7_19389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn7_19389/06_2025/8rn7_19389.cif" } resolution = 3.09 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= -0.001 sd= 0.084 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 Mg 1 5.21 5 S 101 5.16 5 C 7685 2.51 5 N 2073 2.21 5 O 2245 1.98 5 H 12184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24289 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 8275 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 21, 'TRANS': 496} Chain: "B" Number of atoms: 11267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11267 Classifications: {'peptide': 718} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 684} Chain breaks: 4 Chain: "C" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3921 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain breaks: 2 Chain: "D" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 379 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "E" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 446 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.98, per 1000 atoms: 0.53 Number of scatterers: 24289 At special positions: 0 Unit cell: (114.24, 110.04, 113.4, 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 101 16.00 Mg 1 11.99 O 2245 8.00 N 2073 7.00 C 7685 6.00 H 12184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2844 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 16 sheets defined 52.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.585A pdb=" N ALA A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 410 removed outlier: 4.410A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 448 removed outlier: 4.609A pdb=" N TYR A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.582A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.224A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.871A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 4.106A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 removed outlier: 3.700A pdb=" N MET A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 714 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.930A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 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 116 removed outlier: 3.748A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.836A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 266 removed outlier: 4.254A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 293 Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.541A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 454 through 472 Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 539 through 558 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.199A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 632 through 639 removed outlier: 3.532A pdb=" N ILE B 636 " --> pdb=" O HIS B 633 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU B 637 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY B 638 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 665 removed outlier: 3.789A pdb=" N TRP B 665 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 699 Processing helix chain 'B' and resid 712 through 731 removed outlier: 3.595A pdb=" N ALA B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 750 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 44 through 55 removed outlier: 3.789A pdb=" N CYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 55 " --> pdb=" O TRP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.643A pdb=" N ASN C 68 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.810A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.543A pdb=" N LEU C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.003A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'D' and resid 369 through 375 removed outlier: 4.364A pdb=" N PHE D 374 " --> pdb=" O PRO D 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 366 removed outlier: 3.808A pdb=" N TRP E 364 " --> pdb=" O ASN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.247A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 521 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.247A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.696A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.048A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'B' and resid 178 through 188 Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 243 removed outlier: 4.013A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 641 through 642 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 136 removed outlier: 5.436A pdb=" N TRP C 132 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS C 247 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG C 134 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 148 Processing sheet with id=AB7, first strand: chain 'D' and resid 355 through 359 621 hydrogen bonds defined for protein. 1704 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: 9.68 Time building geometry restraints manager: 7.10 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: 12152 1.03 - 1.23: 33 1.23 - 1.42: 5026 1.42 - 1.62: 7147 1.62 - 1.81: 170 Bond restraints: 24528 Sorted by residual: bond pdb=" N PRO C 157 " pdb=" CA PRO C 157 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 9.30e-01 bond pdb=" CB GLN B 104 " pdb=" CG GLN B 104 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.82e-01 bond pdb=" C ASN B 4 " pdb=" O ASN B 4 " ideal model delta sigma weight residual 1.249 1.241 0.007 8.50e-03 1.38e+04 7.39e-01 bond pdb=" C ASN B 628 " pdb=" O ASN B 628 " ideal model delta sigma weight residual 1.238 1.249 -0.011 1.28e-02 6.10e+03 7.14e-01 bond pdb=" CA TRP B 437 " pdb=" CB TRP B 437 " ideal model delta sigma weight residual 1.534 1.553 -0.019 2.33e-02 1.84e+03 6.44e-01 ... (remaining 24523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 42653 1.21 - 2.41: 1619 2.41 - 3.62: 113 3.62 - 4.82: 22 4.82 - 6.03: 1 Bond angle restraints: 44408 Sorted by residual: angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 112.96 109.73 3.23 1.00e+00 1.00e+00 1.04e+01 angle pdb=" N VAL B 516 " pdb=" CA VAL B 516 " pdb=" C VAL B 516 " ideal model delta sigma weight residual 109.34 115.37 -6.03 2.08e+00 2.31e-01 8.40e+00 angle pdb=" N TRP B 309 " pdb=" CA TRP B 309 " pdb=" CB TRP B 309 " ideal model delta sigma weight residual 113.65 109.46 4.19 1.47e+00 4.63e-01 8.13e+00 angle pdb=" CA GLY B 512 " pdb=" C GLY B 512 " pdb=" N VAL B 513 " ideal model delta sigma weight residual 115.34 117.55 -2.21 8.10e-01 1.52e+00 7.44e+00 angle pdb=" CA VAL A 428 " pdb=" C VAL A 428 " pdb=" N ALA A 429 " ideal model delta sigma weight residual 116.60 120.12 -3.52 1.45e+00 4.76e-01 5.90e+00 ... (remaining 44403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 9983 17.30 - 34.60: 1057 34.60 - 51.89: 344 51.89 - 69.19: 90 69.19 - 86.49: 16 Dihedral angle restraints: 11490 sinusoidal: 6357 harmonic: 5133 Sorted by residual: dihedral pdb=" CA GLY B 515 " pdb=" C GLY B 515 " pdb=" N VAL B 516 " pdb=" CA VAL B 516 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA LYS A 327 " pdb=" C LYS A 327 " pdb=" N SER A 328 " pdb=" CA SER A 328 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASP A 678 " pdb=" CB ASP A 678 " pdb=" CG ASP A 678 " pdb=" OD1 ASP A 678 " ideal model delta sinusoidal sigma weight residual -30.00 -87.67 57.67 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 11487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1218 0.029 - 0.058: 432 0.058 - 0.087: 99 0.087 - 0.117: 59 0.117 - 0.146: 18 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE D 368 " pdb=" N ILE D 368 " pdb=" C ILE D 368 " pdb=" CB ILE D 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 376 " pdb=" N ILE B 376 " pdb=" C ILE B 376 " pdb=" CB ILE B 376 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1823 not shown) Planarity restraints: 3571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 253 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO A 254 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 429 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 430 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 444 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C ASP B 444 " -0.026 2.00e-02 2.50e+03 pdb=" O ASP B 444 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 445 " 0.009 2.00e-02 2.50e+03 ... (remaining 3568 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1106 2.17 - 2.77: 48009 2.77 - 3.38: 69651 3.38 - 3.99: 88946 3.99 - 4.60: 140435 Nonbonded interactions: 348147 Sorted by model distance: nonbonded pdb=" OE1 GLU C 111 " pdb=" H GLU C 111 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASP B 454 " pdb=" H THR B 457 " model vdw 1.577 2.450 nonbonded pdb=" O SER B 58 " pdb=" H GLY B 62 " model vdw 1.587 2.450 nonbonded pdb=" H GLY A 237 " pdb=" OE1 GLU B 90 " model vdw 1.600 2.450 nonbonded pdb=" OD2 ASP B 445 " pdb=" H THR B 492 " model vdw 1.602 2.450 ... (remaining 348142 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.840 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: 0.380 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 53.520 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.002 0.027 12344 Z= 0.107 Angle : 0.484 6.029 16635 Z= 0.258 Chirality : 0.036 0.146 1826 Planarity : 0.003 0.052 2127 Dihedral : 16.657 86.490 4693 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 20.42 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.22), residues: 1502 helix: 1.97 (0.20), residues: 704 sheet: -1.26 (0.39), residues: 153 loop : -0.24 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 309 HIS 0.002 0.001 HIS B 561 PHE 0.012 0.001 PHE A 442 TYR 0.009 0.001 TYR B 556 ARG 0.004 0.000 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.12306 ( 616) hydrogen bonds : angle 5.04204 ( 1704) covalent geometry : bond 0.00240 (12344) covalent geometry : angle 0.48364 (16635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.922 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: A 473 MET cc_start: 0.6205 (pmm) cc_final: 0.5571 (pmm) REVERT: A 580 SER cc_start: 0.7807 (m) cc_final: 0.7323 (p) REVERT: C 117 TYR cc_start: 0.6303 (m-80) cc_final: 0.5895 (m-10) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.5454 time to fit residues: 156.6233 Evaluate side-chains 194 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.169026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133879 restraints weight = 47190.895| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.36 r_work: 0.3521 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12344 Z= 0.271 Angle : 0.582 6.389 16635 Z= 0.315 Chirality : 0.042 0.158 1826 Planarity : 0.005 0.061 2127 Dihedral : 4.146 29.219 1643 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.26 % Allowed : 18.69 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.25 (0.21), residues: 1502 helix: 1.27 (0.19), residues: 702 sheet: -1.32 (0.39), residues: 150 loop : -0.63 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 309 HIS 0.004 0.001 HIS C 235 PHE 0.021 0.002 PHE A 709 TYR 0.020 0.002 TYR A 313 ARG 0.004 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 616) hydrogen bonds : angle 4.60767 ( 1704) covalent geometry : bond 0.00642 (12344) covalent geometry : angle 0.58249 (16635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.8747 (mp) cc_final: 0.8372 (mm) REVERT: A 545 PHE cc_start: 0.8129 (m-80) cc_final: 0.7397 (m-80) REVERT: A 580 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7372 (p) REVERT: B 246 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8556 (tp) REVERT: B 437 TRP cc_start: 0.9082 (OUTLIER) cc_final: 0.8831 (p90) REVERT: B 572 MET cc_start: 0.6283 (mmm) cc_final: 0.5203 (mmm) REVERT: C 245 ILE cc_start: 0.8077 (mt) cc_final: 0.7779 (mp) outliers start: 30 outliers final: 19 residues processed: 228 average time/residue: 0.5214 time to fit residues: 174.9494 Evaluate side-chains 223 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN C 102 ASN C 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.173625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138617 restraints weight = 46308.841| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.36 r_work: 0.3567 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12344 Z= 0.114 Angle : 0.486 5.675 16635 Z= 0.255 Chirality : 0.037 0.160 1826 Planarity : 0.004 0.058 2127 Dihedral : 3.917 27.369 1643 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 1.36 % Allowed : 20.05 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.65 (0.22), residues: 1502 helix: 1.67 (0.20), residues: 690 sheet: -1.25 (0.38), residues: 157 loop : -0.42 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.002 0.000 HIS A 462 PHE 0.010 0.001 PHE A 442 TYR 0.012 0.001 TYR A 313 ARG 0.002 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 616) hydrogen bonds : angle 4.26236 ( 1704) covalent geometry : bond 0.00262 (12344) covalent geometry : angle 0.48621 (16635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.8691 (mp) cc_final: 0.8350 (mm) REVERT: A 473 MET cc_start: 0.6291 (pmm) cc_final: 0.5773 (pmm) REVERT: A 545 PHE cc_start: 0.8020 (m-80) cc_final: 0.7368 (m-80) REVERT: A 580 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7275 (p) REVERT: B 246 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 572 MET cc_start: 0.6269 (mmm) cc_final: 0.5316 (mmm) outliers start: 18 outliers final: 12 residues processed: 217 average time/residue: 0.5207 time to fit residues: 166.0577 Evaluate side-chains 214 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 148 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.170563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135112 restraints weight = 47171.556| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.41 r_work: 0.3524 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12344 Z= 0.197 Angle : 0.529 5.703 16635 Z= 0.281 Chirality : 0.039 0.158 1826 Planarity : 0.004 0.059 2127 Dihedral : 4.086 29.880 1643 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 2.49 % Allowed : 19.07 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.36 (0.21), residues: 1502 helix: 1.38 (0.20), residues: 701 sheet: -1.24 (0.39), residues: 155 loop : -0.60 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 309 HIS 0.003 0.001 HIS B 47 PHE 0.015 0.001 PHE A 709 TYR 0.020 0.002 TYR A 313 ARG 0.002 0.000 ARG A 540 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 616) hydrogen bonds : angle 4.35646 ( 1704) covalent geometry : bond 0.00467 (12344) covalent geometry : angle 0.52920 (16635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.8687 (mp) cc_final: 0.8334 (mm) REVERT: A 473 MET cc_start: 0.6387 (pmm) cc_final: 0.5951 (pmm) REVERT: A 545 PHE cc_start: 0.8146 (m-80) cc_final: 0.7470 (m-80) REVERT: A 580 SER cc_start: 0.7881 (OUTLIER) cc_final: 0.7334 (p) REVERT: B 239 ARG cc_start: 0.4809 (OUTLIER) cc_final: 0.4556 (ptp-170) REVERT: B 246 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8541 (tp) REVERT: B 437 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.8887 (p90) REVERT: B 705 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5928 (ttt180) REVERT: C 101 TRP cc_start: 0.3792 (t-100) cc_final: 0.3401 (t-100) outliers start: 33 outliers final: 22 residues processed: 229 average time/residue: 0.5199 time to fit residues: 174.7844 Evaluate side-chains 228 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136876 restraints weight = 46702.617| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.38 r_work: 0.3546 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12344 Z= 0.124 Angle : 0.487 5.543 16635 Z= 0.256 Chirality : 0.038 0.159 1826 Planarity : 0.004 0.056 2127 Dihedral : 3.983 27.973 1643 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 2.03 % Allowed : 19.52 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.51 (0.22), residues: 1502 helix: 1.55 (0.20), residues: 696 sheet: -1.34 (0.38), residues: 145 loop : -0.53 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.003 0.001 HIS A 643 PHE 0.013 0.001 PHE A 442 TYR 0.012 0.001 TYR A 313 ARG 0.002 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 616) hydrogen bonds : angle 4.21375 ( 1704) covalent geometry : bond 0.00291 (12344) covalent geometry : angle 0.48712 (16635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8412 (mtmm) REVERT: A 323 ILE cc_start: 0.8671 (mp) cc_final: 0.8319 (mm) REVERT: A 473 MET cc_start: 0.6479 (pmm) cc_final: 0.6035 (pmm) REVERT: A 545 PHE cc_start: 0.8092 (m-80) cc_final: 0.7429 (m-80) REVERT: A 580 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7291 (p) REVERT: B 239 ARG cc_start: 0.4792 (OUTLIER) cc_final: 0.4564 (ptp-170) REVERT: B 246 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8508 (tp) REVERT: C 101 TRP cc_start: 0.3798 (t-100) cc_final: 0.3504 (t-100) outliers start: 27 outliers final: 19 residues processed: 220 average time/residue: 0.5385 time to fit residues: 172.5726 Evaluate side-chains 217 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 5 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136749 restraints weight = 46850.378| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.35 r_work: 0.3545 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12344 Z= 0.140 Angle : 0.490 5.847 16635 Z= 0.257 Chirality : 0.038 0.157 1826 Planarity : 0.004 0.055 2127 Dihedral : 3.972 29.422 1643 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 1.88 % Allowed : 19.74 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.53 (0.22), residues: 1502 helix: 1.57 (0.20), residues: 696 sheet: -1.33 (0.38), residues: 145 loop : -0.52 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS A 643 PHE 0.012 0.001 PHE A 442 TYR 0.012 0.001 TYR B 556 ARG 0.002 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 616) hydrogen bonds : angle 4.19605 ( 1704) covalent geometry : bond 0.00331 (12344) covalent geometry : angle 0.48975 (16635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8458 (mtmm) REVERT: A 323 ILE cc_start: 0.8697 (mp) cc_final: 0.8343 (mm) REVERT: A 360 ASN cc_start: 0.8065 (t0) cc_final: 0.7857 (t0) REVERT: A 473 MET cc_start: 0.6481 (pmm) cc_final: 0.6076 (pmm) REVERT: A 545 PHE cc_start: 0.8076 (m-80) cc_final: 0.7434 (m-80) REVERT: A 580 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7353 (p) REVERT: B 239 ARG cc_start: 0.4913 (OUTLIER) cc_final: 0.4664 (ptp-170) REVERT: B 246 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8520 (tp) REVERT: C 101 TRP cc_start: 0.3795 (t-100) cc_final: 0.3457 (t-100) outliers start: 25 outliers final: 21 residues processed: 218 average time/residue: 0.5932 time to fit residues: 192.8875 Evaluate side-chains 222 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 74 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138326 restraints weight = 46669.596| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.36 r_work: 0.3561 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12344 Z= 0.106 Angle : 0.472 5.218 16635 Z= 0.246 Chirality : 0.037 0.158 1826 Planarity : 0.004 0.053 2127 Dihedral : 3.863 27.830 1643 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 1.96 % Allowed : 20.57 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.69 (0.22), residues: 1502 helix: 1.73 (0.20), residues: 697 sheet: -1.22 (0.38), residues: 146 loop : -0.47 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.005 0.001 HIS B 745 PHE 0.013 0.001 PHE A 442 TYR 0.010 0.001 TYR B 466 ARG 0.002 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 616) hydrogen bonds : angle 4.08306 ( 1704) covalent geometry : bond 0.00248 (12344) covalent geometry : angle 0.47250 (16635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8452 (mtmm) REVERT: A 468 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 473 MET cc_start: 0.6338 (pmm) cc_final: 0.5956 (pmm) REVERT: A 545 PHE cc_start: 0.8107 (m-80) cc_final: 0.7491 (m-80) REVERT: A 580 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7367 (p) REVERT: B 246 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8500 (tp) REVERT: C 101 TRP cc_start: 0.3707 (t-100) cc_final: 0.3358 (t-100) REVERT: C 211 ARG cc_start: 0.7113 (ttm110) cc_final: 0.6750 (ttm-80) outliers start: 26 outliers final: 19 residues processed: 219 average time/residue: 0.5249 time to fit residues: 169.1826 Evaluate side-chains 217 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 50.9488 > 50: distance: 89 - 100: 5.399 distance: 90 - 91: 3.137 distance: 90 - 101: 3.759 distance: 91 - 92: 5.380 distance: 91 - 113: 3.507 distance: 93 - 103: 3.827 distance: 94 - 95: 3.392 distance: 94 - 104: 4.078 distance: 95 - 106: 5.422 distance: 95 - 107: 3.858 distance: 97 - 98: 3.070 distance: 98 - 110: 3.159 distance: 113 - 114: 6.496 distance: 113 - 120: 9.099 distance: 114 - 115: 3.773 distance: 114 - 117: 4.343 distance: 114 - 121: 7.538 distance: 115 - 116: 3.318 distance: 117 - 118: 4.123 distance: 117 - 119: 3.810 distance: 117 - 122: 3.213 distance: 118 - 123: 3.810 distance: 118 - 124: 3.602 distance: 119 - 126: 3.194 distance: 119 - 127: 3.096 distance: 129 - 130: 3.602 distance: 129 - 137: 9.417 distance: 130 - 133: 4.078 distance: 130 - 138: 7.088 distance: 131 - 132: 3.066 distance: 131 - 143: 6.543 distance: 133 - 139: 4.197 distance: 133 - 140: 6.235 distance: 134 - 135: 3.679 distance: 134 - 136: 3.255 distance: 136 - 142: 4.112 distance: 143 - 144: 5.686 distance: 143 - 149: 5.893 distance: 144 - 145: 7.697 distance: 144 - 147: 8.075 distance: 144 - 150: 5.566 distance: 145 - 146: 14.605 distance: 145 - 154: 9.218 distance: 147 - 148: 5.415 distance: 147 - 151: 5.943 distance: 147 - 152: 5.812 distance: 148 - 153: 4.960 distance: 154 - 155: 12.249 distance: 154 - 160: 4.207 distance: 155 - 156: 6.632 distance: 155 - 158: 7.437 distance: 155 - 161: 6.542 distance: 156 - 157: 16.719 distance: 156 - 168: 10.964 distance: 158 - 159: 4.156 distance: 158 - 162: 11.414 distance: 158 - 163: 7.521 distance: 159 - 160: 6.479 distance: 159 - 164: 15.901 distance: 159 - 165: 3.014 distance: 160 - 166: 10.559 distance: 160 - 167: 13.769 distance: 168 - 169: 7.800 distance: 168 - 177: 16.254 distance: 169 - 170: 8.451 distance: 169 - 172: 8.359 distance: 169 - 178: 15.940 distance: 170 - 171: 6.354 distance: 172 - 173: 4.212 distance: 172 - 179: 14.709 distance: 172 - 180: 19.891 distance: 173 - 174: 3.440 distance: 173 - 181: 3.327 distance: 173 - 182: 10.964 distance: 174 - 183: 9.906 distance: 174 - 184: 9.170 distance: 175 - 176: 3.465 distance: 175 - 185: 7.999 distance: 176 - 187: 6.187 distance: 176 - 188: 3.839 distance: 176 - 189: 5.644 distance: 190 - 191: 9.217 distance: 190 - 197: 17.900 distance: 191 - 192: 6.265 distance: 191 - 194: 3.591 distance: 191 - 198: 4.537 distance: 192 - 193: 7.007 distance: 192 - 204: 6.067 distance: 194 - 196: 8.100 distance: 194 - 199: 3.764 distance: 195 - 200: 7.963 distance: 196 - 201: 7.494 distance: 196 - 202: 11.966 distance: 196 - 203: 7.703 distance: 204 - 205: 3.715 distance: 204 - 215: 8.320 distance: 204 - 307: 4.882 distance: 205 - 206: 5.683 distance: 205 - 208: 3.510 distance: 205 - 216: 6.041 distance: 206 - 207: 8.318 distance: 206 - 224: 11.982 distance: 207 - 304: 4.523 distance: 208 - 209: 3.973 distance: 208 - 217: 10.110 distance: 208 - 218: 6.314 distance: 209 - 210: 6.063 distance: 210 - 219: 4.084 distance: 224 - 225: 12.376 distance: 224 - 230: 10.893 distance: 225 - 226: 13.547 distance: 225 - 228: 10.149 distance: 225 - 231: 4.933 distance: 226 - 227: 22.936 distance: 226 - 235: 22.130 distance: 228 - 229: 4.779 distance: 228 - 232: 7.315 distance: 228 - 233: 6.397 distance: 229 - 234: 10.972 distance: 235 - 236: 13.453 distance: 235 - 243: 25.062 distance: 235 - 274: 12.483 distance: 236 - 237: 14.523 distance: 236 - 239: 11.878 distance: 236 - 244: 15.357 distance: 237 - 238: 9.199 distance: 237 - 254: 9.913 distance: 239 - 240: 4.291 distance: 239 - 241: 8.744 distance: 239 - 245: 5.981 distance: 240 - 242: 4.052 distance: 240 - 247: 10.139 distance: 241 - 248: 3.762 distance: 241 - 249: 8.048 distance: 241 - 250: 7.364 distance: 242 - 251: 3.739 distance: 242 - 252: 3.779