Starting phenix.real_space_refine on Sat Jan 18 01:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdy_37467/01_2025/8wdy_37467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdy_37467/01_2025/8wdy_37467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wdy_37467/01_2025/8wdy_37467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdy_37467/01_2025/8wdy_37467.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdy_37467/01_2025/8wdy_37467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdy_37467/01_2025/8wdy_37467.cif" } resolution = 2.69 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6322 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4188 2.51 5 N 1073 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6548 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1549 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.28, per 1000 atoms: 0.65 Number of scatterers: 6548 At special positions: 0 Unit cell: (74.8, 85.85, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1249 8.00 N 1073 7.00 C 4188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 890.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 53.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.527A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.567A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.200A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.026A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.510A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.671A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 249 removed outlier: 4.009A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.795A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.608A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.887A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.742A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.503A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.577A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.537A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.741A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.652A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.859A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.012A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.251A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.116A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.896A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 278 hydrogen bonds defined for protein. 789 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: 1.70 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2059 1.34 - 1.47: 1746 1.47 - 1.59: 2868 1.59 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6731 Sorted by residual: bond pdb=" CE1 HIS A 34 " pdb=" NE2 HIS A 34 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" C HIS A 34 " pdb=" N GLU A 35 " ideal model delta sigma weight residual 1.334 1.288 0.046 1.20e-02 6.94e+03 1.50e+01 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.15e+01 bond pdb=" N HIS A 34 " pdb=" CA HIS A 34 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.17e-02 7.31e+03 1.14e+01 ... (remaining 6726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 8940 2.35 - 4.70: 182 4.70 - 7.06: 25 7.06 - 9.41: 4 9.41 - 11.76: 1 Bond angle restraints: 9152 Sorted by residual: angle pdb=" N HIS A 34 " pdb=" CA HIS A 34 " pdb=" C HIS A 34 " ideal model delta sigma weight residual 112.72 100.96 11.76 1.28e+00 6.10e-01 8.44e+01 angle pdb=" C HIS A 34 " pdb=" N GLU A 35 " pdb=" CA GLU A 35 " ideal model delta sigma weight residual 120.79 129.77 -8.98 1.39e+00 5.18e-01 4.18e+01 angle pdb=" N THR A 92 " pdb=" CA THR A 92 " pdb=" C THR A 92 " ideal model delta sigma weight residual 113.41 106.00 7.41 1.22e+00 6.72e-01 3.69e+01 angle pdb=" O ASN A 33 " pdb=" C ASN A 33 " pdb=" N HIS A 34 " ideal model delta sigma weight residual 122.59 115.99 6.60 1.33e+00 5.65e-01 2.46e+01 angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 113.50 107.53 5.97 1.23e+00 6.61e-01 2.35e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 3860 24.77 - 49.53: 195 49.53 - 74.30: 29 74.30 - 99.06: 11 99.06 - 123.83: 1 Dihedral angle restraints: 4096 sinusoidal: 1774 harmonic: 2322 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 27.76 65.24 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CA GLU A 145 " pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual 0.00 -28.16 28.16 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 60.87 -123.83 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 4093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 832 0.060 - 0.119: 136 0.119 - 0.178: 13 0.178 - 0.238: 5 0.238 - 0.297: 1 Chirality restraints: 987 Sorted by residual: chirality pdb=" CA HIS A 34 " pdb=" N HIS A 34 " pdb=" C HIS A 34 " pdb=" CB HIS A 34 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA TYR B 501 " pdb=" N TYR B 501 " pdb=" C TYR B 501 " pdb=" CB TYR B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TYR B 453 " pdb=" N TYR B 453 " pdb=" C TYR B 453 " pdb=" CB TYR B 453 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 984 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 34 " 0.042 2.00e-02 2.50e+03 9.01e-02 8.11e+01 pdb=" C HIS A 34 " -0.156 2.00e-02 2.50e+03 pdb=" O HIS A 34 " 0.059 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 484 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ALA B 484 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA B 484 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY B 485 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 85 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LEU A 85 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 85 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN A 86 " -0.020 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 42 2.58 - 3.16: 5172 3.16 - 3.74: 9722 3.74 - 4.32: 13544 4.32 - 4.90: 22870 Nonbonded interactions: 51350 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 2.000 2.230 nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.173 3.040 nonbonded pdb=" OG SER A 425 " pdb=" OD1 ASP A 427 " model vdw 2.186 3.040 nonbonded pdb=" NE2 GLN A 42 " pdb=" NH2 ARG B 498 " model vdw 2.234 3.200 nonbonded pdb=" OG1 THR A 20 " pdb=" OE1 GLU A 23 " model vdw 2.269 3.040 ... (remaining 51345 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 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 0.070 6731 Z= 0.276 Angle : 0.762 11.760 9152 Z= 0.478 Chirality : 0.047 0.297 987 Planarity : 0.005 0.090 1173 Dihedral : 14.720 123.825 2585 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 1.44 % Allowed : 0.87 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.26 (0.31), residues: 787 helix: 1.05 (0.28), residues: 383 sheet: 1.83 (0.79), residues: 44 loop : -1.02 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.035 0.001 PHE A 592 TYR 0.044 0.001 TYR B 453 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.7107 (tmm) cc_final: 0.6699 (tmm) REVERT: B 406 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 509 ARG cc_start: 0.8448 (mtt180) cc_final: 0.8230 (mtt-85) outliers start: 10 outliers final: 3 residues processed: 191 average time/residue: 1.1564 time to fit residues: 232.4884 Evaluate side-chains 166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 61 ASN A 64 ASN A 598 GLN B 437 ASN B 487 ASN B 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114733 restraints weight = 8962.525| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.94 r_work: 0.3431 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6731 Z= 0.223 Angle : 0.553 10.868 9152 Z= 0.280 Chirality : 0.043 0.234 987 Planarity : 0.004 0.051 1173 Dihedral : 8.564 108.731 1070 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 10.97 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.44 (0.31), residues: 787 helix: 1.30 (0.28), residues: 377 sheet: 1.72 (0.75), residues: 44 loop : -0.97 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE A 400 TYR 0.017 0.001 TYR A 202 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6846 (mp0) cc_final: 0.6456 (mp0) REVERT: A 364 VAL cc_start: 0.8332 (m) cc_final: 0.8109 (t) REVERT: A 431 ASP cc_start: 0.7622 (p0) cc_final: 0.7409 (p0) REVERT: A 455 MET cc_start: 0.7655 (tmm) cc_final: 0.7308 (tmm) REVERT: A 496 THR cc_start: 0.8794 (m) cc_final: 0.8555 (t) REVERT: B 343 ASN cc_start: 0.7731 (t0) cc_final: 0.7380 (t0) outliers start: 10 outliers final: 3 residues processed: 172 average time/residue: 1.1575 time to fit residues: 210.0315 Evaluate side-chains 166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 67 optimal weight: 0.0270 chunk 45 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 409 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115401 restraints weight = 9065.361| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.94 r_work: 0.3440 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6731 Z= 0.157 Angle : 0.503 8.193 9152 Z= 0.251 Chirality : 0.041 0.221 987 Planarity : 0.004 0.039 1173 Dihedral : 7.703 105.503 1065 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 13.13 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.58 (0.31), residues: 787 helix: 1.53 (0.28), residues: 371 sheet: 1.33 (0.75), residues: 44 loop : -0.94 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.007 0.001 PHE A 72 TYR 0.016 0.001 TYR A 202 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8056 (t) REVERT: A 455 MET cc_start: 0.7629 (tmm) cc_final: 0.7288 (tmm) REVERT: B 343 ASN cc_start: 0.7657 (t0) cc_final: 0.7273 (t0) outliers start: 14 outliers final: 8 residues processed: 165 average time/residue: 1.2137 time to fit residues: 210.7541 Evaluate side-chains 168 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112820 restraints weight = 9138.899| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.96 r_work: 0.3399 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6731 Z= 0.289 Angle : 0.561 9.766 9152 Z= 0.280 Chirality : 0.044 0.223 987 Planarity : 0.004 0.039 1173 Dihedral : 7.364 97.960 1065 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.45 % Allowed : 13.42 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.50 (0.31), residues: 787 helix: 1.46 (0.28), residues: 371 sheet: 1.13 (0.74), residues: 44 loop : -0.95 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE A 400 TYR 0.015 0.002 TYR A 202 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8364 (tmm) cc_final: 0.8116 (ttp) REVERT: A 364 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8149 (t) REVERT: A 455 MET cc_start: 0.7738 (tmm) cc_final: 0.7297 (tmm) REVERT: A 564 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: B 343 ASN cc_start: 0.7704 (t0) cc_final: 0.7271 (t0) outliers start: 17 outliers final: 9 residues processed: 171 average time/residue: 1.1453 time to fit residues: 206.0234 Evaluate side-chains 174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.0050 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 0.0040 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114516 restraints weight = 9081.383| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.92 r_work: 0.3424 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6731 Z= 0.175 Angle : 0.528 9.400 9152 Z= 0.262 Chirality : 0.042 0.212 987 Planarity : 0.004 0.037 1173 Dihedral : 6.953 90.799 1065 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 14.57 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.62 (0.31), residues: 787 helix: 1.56 (0.28), residues: 373 sheet: 0.90 (0.74), residues: 44 loop : -0.88 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 PHE 0.009 0.001 PHE A 315 TYR 0.014 0.001 TYR A 202 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7927 (tp30) cc_final: 0.7638 (tp30) REVERT: A 190 MET cc_start: 0.8348 (tmm) cc_final: 0.8061 (ttp) REVERT: A 364 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8118 (t) REVERT: A 383 MET cc_start: 0.8423 (mtp) cc_final: 0.8142 (mtp) REVERT: A 455 MET cc_start: 0.7677 (tmm) cc_final: 0.7272 (tmm) REVERT: A 564 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: B 343 ASN cc_start: 0.7650 (t0) cc_final: 0.7228 (t0) outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 1.1870 time to fit residues: 203.5132 Evaluate side-chains 161 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 72.0439 > 50: distance: 25 - 170: 34.023 distance: 28 - 167: 36.742 distance: 68 - 89: 37.207 distance: 85 - 89: 34.230 distance: 89 - 90: 40.005 distance: 90 - 91: 58.063 distance: 90 - 93: 40.498 distance: 91 - 92: 56.443 distance: 91 - 97: 39.043 distance: 94 - 95: 40.267 distance: 94 - 96: 40.044 distance: 97 - 98: 41.127 distance: 98 - 99: 40.540 distance: 98 - 101: 39.277 distance: 99 - 100: 40.208 distance: 99 - 109: 39.804 distance: 102 - 103: 39.318 distance: 103 - 105: 39.033 distance: 105 - 107: 39.773 distance: 106 - 107: 69.428 distance: 110 - 111: 41.529 distance: 111 - 112: 57.215 distance: 115 - 116: 41.391 distance: 116 - 117: 56.097 distance: 118 - 119: 55.971 distance: 119 - 120: 68.421 distance: 119 - 122: 58.071 distance: 120 - 121: 38.958 distance: 120 - 126: 70.523 distance: 123 - 124: 56.641 distance: 126 - 127: 39.539 distance: 126 - 132: 39.028 distance: 127 - 128: 39.024 distance: 127 - 130: 57.345 distance: 128 - 129: 40.832 distance: 128 - 133: 38.791 distance: 130 - 131: 39.949 distance: 131 - 132: 39.648 distance: 133 - 134: 41.008 distance: 134 - 135: 41.257 distance: 134 - 137: 30.563 distance: 135 - 136: 57.107 distance: 135 - 141: 38.675 distance: 138 - 139: 56.265 distance: 138 - 140: 40.268 distance: 141 - 142: 41.048 distance: 142 - 143: 39.907 distance: 142 - 145: 56.282 distance: 146 - 147: 56.476 distance: 150 - 151: 40.713 distance: 150 - 153: 39.107 distance: 151 - 152: 40.398 distance: 153 - 154: 39.689 distance: 154 - 155: 40.990 distance: 157 - 159: 57.169 distance: 158 - 159: 39.092 distance: 161 - 162: 55.464 distance: 161 - 164: 70.250 distance: 162 - 163: 40.646 distance: 162 - 167: 70.337 distance: 167 - 168: 55.439 distance: 168 - 169: 57.830 distance: 169 - 170: 40.699 distance: 169 - 171: 33.833