Starting phenix.real_space_refine on Wed Mar 12 19:06:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsl_30837/03_2025/7dsl_30837_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsl_30837/03_2025/7dsl_30837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2025/7dsl_30837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2025/7dsl_30837.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2025/7dsl_30837_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2025/7dsl_30837_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 4938 2.51 5 N 1191 2.21 5 O 1365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7522 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3670 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} 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: 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: "E" 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: "F" 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: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 106 Unusual residues: {'HO0': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 8} Link IDs: {None: 10} Time building chain proxies: 5.44, per 1000 atoms: 0.72 Number of scatterers: 7522 At special positions: 0 Unit cell: (81.525, 83.699, 126.092, 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) S 27 16.00 P 1 15.00 O 1365 8.00 N 1191 7.00 C 4938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.04 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 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 819.7 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 58.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 206 removed outlier: 3.647A pdb=" N LEU A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.810A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.594A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.243A pdb=" N VAL A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.948A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.505A pdb=" N ILE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.673A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.603A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.571A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.670A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.832A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 80 removed outlier: 3.810A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.650A pdb=" N ALA B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 removed outlier: 4.909A pdb=" N TYR B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 167 through 189 Processing helix chain 'B' and resid 189 through 221 removed outlier: 3.647A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 253 removed outlier: 3.713A pdb=" N ILE B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.988A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 400 through 421 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.526A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.922A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 477 Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.794A pdb=" N LEU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.570A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.527A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 627 " --> pdb=" O ARG A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA6, first strand: chain 'B' and resid 365 through 366 393 hydrogen bonds defined for protein. 1128 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: 1.97 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1170 1.31 - 1.43: 2066 1.43 - 1.56: 4401 1.56 - 1.68: 25 1.68 - 1.81: 41 Bond restraints: 7703 Sorted by residual: bond pdb=" C02 HO0 B 601 " pdb=" C07 HO0 B 601 " ideal model delta sigma weight residual 1.508 1.753 -0.245 2.00e-02 2.50e+03 1.51e+02 bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C09 HO0 B 601 " pdb=" C10 HO0 B 601 " ideal model delta sigma weight residual 1.522 1.341 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" CBG Y01 B 602 " pdb=" CBI Y01 B 602 " ideal model delta sigma weight residual 1.537 1.383 0.154 2.00e-02 2.50e+03 5.92e+01 ... (remaining 7698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 10173 3.16 - 6.32: 264 6.32 - 9.48: 41 9.48 - 12.64: 9 12.64 - 15.80: 3 Bond angle restraints: 10490 Sorted by residual: angle pdb=" N SER B 143 " pdb=" CA SER B 143 " pdb=" C SER B 143 " ideal model delta sigma weight residual 113.18 105.23 7.95 1.33e+00 5.65e-01 3.57e+01 angle pdb=" N THR B 71 " pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 109.81 121.94 -12.13 2.21e+00 2.05e-01 3.01e+01 angle pdb=" C03 HO0 B 601 " pdb=" C10 HO0 B 601 " pdb=" C09 HO0 B 601 " ideal model delta sigma weight residual 113.02 128.82 -15.80 3.00e+00 1.11e-01 2.77e+01 angle pdb=" C08 HO0 B 601 " pdb=" C09 HO0 B 601 " pdb=" C10 HO0 B 601 " ideal model delta sigma weight residual 111.81 127.13 -15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" N LEU B 282 " pdb=" CA LEU B 282 " pdb=" C LEU B 282 " ideal model delta sigma weight residual 109.81 120.96 -11.15 2.21e+00 2.05e-01 2.54e+01 ... (remaining 10485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 4531 35.08 - 70.16: 140 70.16 - 105.24: 24 105.24 - 140.32: 34 140.32 - 175.40: 8 Dihedral angle restraints: 4737 sinusoidal: 2057 harmonic: 2680 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual -86.00 -148.65 62.65 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CA LYS B 479 " pdb=" C LYS B 479 " pdb=" N ASN B 480 " pdb=" CA ASN B 480 " ideal model delta harmonic sigma weight residual 180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PHE B 231 " pdb=" C PHE B 231 " pdb=" N SER B 232 " pdb=" CA SER B 232 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 4734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.187: 1223 1.187 - 2.374: 0 2.374 - 3.562: 0 3.562 - 4.749: 0 4.749 - 5.936: 10 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -3.00 5.94 2.00e-01 2.50e+01 8.81e+02 chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -2.94 5.88 2.00e-01 2.50e+01 8.65e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.68 -5.53 2.00e-01 2.50e+01 7.64e+02 ... (remaining 1230 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO A 619 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 103 " -0.011 2.00e-02 2.50e+03 1.69e-02 5.68e+00 pdb=" CG TYR B 103 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 103 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 103 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 103 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 103 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 158 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO B 159 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.033 5.00e-02 4.00e+02 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 97 2.62 - 3.19: 6415 3.19 - 3.76: 11313 3.76 - 4.33: 15776 4.33 - 4.90: 25767 Nonbonded interactions: 59368 Sorted by model distance: nonbonded pdb=" O ASP A 408 " pdb=" OG SER A 409 " model vdw 2.055 3.040 nonbonded pdb=" O GLY B 67 " pdb=" OG1 THR B 71 " model vdw 2.214 3.040 nonbonded pdb=" O ILE B 464 " pdb=" OG SER B 467 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 293 " pdb=" OG SER A 297 " model vdw 2.301 3.040 nonbonded pdb=" O PRO B 368 " pdb=" N LEU B 370 " model vdw 2.310 3.120 ... (remaining 59363 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 20.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.013 0.245 7703 Z= 0.815 Angle : 1.259 15.802 10490 Z= 0.672 Chirality : 0.491 5.936 1233 Planarity : 0.007 0.077 1282 Dihedral : 22.636 175.403 3012 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.13 % Favored : 90.01 % Rotamer: Outliers : 1.14 % Allowed : 6.72 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.21), residues: 931 helix: -1.91 (0.18), residues: 495 sheet: -1.27 (0.62), residues: 62 loop : -3.44 (0.24), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 220 HIS 0.005 0.001 HIS A 221 PHE 0.027 0.003 PHE B 351 TYR 0.040 0.003 TYR B 103 ARG 0.010 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.837 Fit side-chains REVERT: A 184 TRP cc_start: 0.8239 (m100) cc_final: 0.7926 (m-10) REVERT: A 360 PHE cc_start: 0.9272 (m-80) cc_final: 0.9070 (m-80) REVERT: A 398 ASP cc_start: 0.7910 (p0) cc_final: 0.7294 (t0) REVERT: B 239 ASP cc_start: 0.7670 (t0) cc_final: 0.7257 (p0) REVERT: B 272 ARG cc_start: 0.8373 (ttt-90) cc_final: 0.8159 (ttt-90) REVERT: B 314 ASP cc_start: 0.8169 (m-30) cc_final: 0.7899 (m-30) REVERT: B 365 MET cc_start: 0.9039 (mtt) cc_final: 0.8631 (mtt) REVERT: B 369 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: B 392 ASP cc_start: 0.7849 (t0) cc_final: 0.7476 (t0) REVERT: B 462 PHE cc_start: 0.8259 (t80) cc_final: 0.7983 (t80) outliers start: 9 outliers final: 1 residues processed: 117 average time/residue: 1.1945 time to fit residues: 148.4793 Evaluate side-chains 65 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 353 ASN A 483 GLN B 230 ASN B 261 ASN B 273 ASN B 398 ASN B 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.075668 restraints weight = 13505.438| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.13 r_work: 0.2774 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7703 Z= 0.202 Angle : 1.269 34.168 10490 Z= 0.503 Chirality : 0.109 1.776 1233 Planarity : 0.005 0.058 1282 Dihedral : 22.951 174.660 1370 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.34 % Favored : 93.13 % Rotamer: Outliers : 2.28 % Allowed : 11.91 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.26), residues: 931 helix: 0.18 (0.23), residues: 506 sheet: -1.05 (0.61), residues: 67 loop : -3.01 (0.27), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 220 HIS 0.008 0.001 HIS B 367 PHE 0.015 0.001 PHE B 351 TYR 0.011 0.001 TYR B 103 ARG 0.005 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.059 Fit side-chains REVERT: A 184 TRP cc_start: 0.8424 (m100) cc_final: 0.7892 (m-10) REVERT: A 269 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8710 (tt0) REVERT: A 398 ASP cc_start: 0.7894 (p0) cc_final: 0.7308 (t0) REVERT: B 137 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 239 ASP cc_start: 0.7693 (t0) cc_final: 0.7157 (p0) REVERT: B 266 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: B 314 ASP cc_start: 0.8218 (m-30) cc_final: 0.7752 (m-30) REVERT: B 365 MET cc_start: 0.9307 (mtt) cc_final: 0.9060 (ttm) REVERT: B 392 ASP cc_start: 0.7916 (t0) cc_final: 0.7630 (t0) REVERT: B 397 ILE cc_start: 0.8945 (pt) cc_final: 0.8734 (pp) REVERT: B 421 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7307 (ptm-80) REVERT: B 451 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: B 500 MET cc_start: 0.8784 (mtt) cc_final: 0.8420 (mtm) REVERT: B 507 THR cc_start: 0.4565 (OUTLIER) cc_final: 0.4264 (p) outliers start: 18 outliers final: 5 residues processed: 88 average time/residue: 1.1626 time to fit residues: 110.9513 Evaluate side-chains 70 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 10 optimal weight: 0.0030 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS B 47 GLN B 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.076776 restraints weight = 13639.335| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.13 r_work: 0.2787 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7703 Z= 0.187 Angle : 1.208 33.034 10490 Z= 0.467 Chirality : 0.108 1.869 1233 Planarity : 0.004 0.051 1282 Dihedral : 22.627 178.289 1367 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.77 % Favored : 92.91 % Rotamer: Outliers : 2.66 % Allowed : 13.31 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.28), residues: 931 helix: 0.96 (0.24), residues: 507 sheet: -0.81 (0.62), residues: 67 loop : -2.57 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 220 HIS 0.005 0.001 HIS B 367 PHE 0.019 0.001 PHE B 474 TYR 0.011 0.001 TYR B 103 ARG 0.005 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.861 Fit side-chains REVERT: A 172 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8847 (ptmt) REVERT: A 184 TRP cc_start: 0.8448 (m100) cc_final: 0.7889 (m-10) REVERT: A 269 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8696 (tt0) REVERT: A 398 ASP cc_start: 0.8038 (p0) cc_final: 0.7456 (t0) REVERT: B 137 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8968 (tt) REVERT: B 239 ASP cc_start: 0.7576 (t0) cc_final: 0.7154 (p0) REVERT: B 266 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: B 314 ASP cc_start: 0.8218 (m-30) cc_final: 0.7861 (m-30) REVERT: B 365 MET cc_start: 0.9325 (mtt) cc_final: 0.9040 (ttm) REVERT: B 392 ASP cc_start: 0.7968 (t0) cc_final: 0.7701 (t0) REVERT: B 397 ILE cc_start: 0.9015 (pt) cc_final: 0.8707 (pp) REVERT: B 421 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7231 (ptm-80) REVERT: B 451 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7737 (m-10) outliers start: 21 outliers final: 9 residues processed: 89 average time/residue: 0.9849 time to fit residues: 94.8160 Evaluate side-chains 73 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.075598 restraints weight = 13658.732| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.15 r_work: 0.2768 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7703 Z= 0.211 Angle : 1.197 33.413 10490 Z= 0.461 Chirality : 0.107 1.803 1233 Planarity : 0.004 0.049 1282 Dihedral : 22.468 179.020 1367 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.09 % Favored : 92.70 % Rotamer: Outliers : 3.42 % Allowed : 14.20 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.28), residues: 931 helix: 1.30 (0.24), residues: 501 sheet: -0.81 (0.60), residues: 67 loop : -2.31 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.005 0.001 HIS B 367 PHE 0.015 0.001 PHE B 351 TYR 0.014 0.001 TYR A 629 ARG 0.003 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.775 Fit side-chains REVERT: A 184 TRP cc_start: 0.8467 (m100) cc_final: 0.7901 (m-10) REVERT: A 269 GLN cc_start: 0.8939 (tp40) cc_final: 0.8722 (tt0) REVERT: A 356 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8033 (p0) REVERT: A 398 ASP cc_start: 0.7768 (p0) cc_final: 0.7330 (OUTLIER) REVERT: B 137 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8969 (tt) REVERT: B 218 GLN cc_start: 0.7876 (tp40) cc_final: 0.7451 (tm-30) REVERT: B 239 ASP cc_start: 0.7595 (t0) cc_final: 0.7272 (p0) REVERT: B 266 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: B 314 ASP cc_start: 0.8266 (m-30) cc_final: 0.7916 (m-30) REVERT: B 365 MET cc_start: 0.9319 (mtt) cc_final: 0.9027 (ttm) REVERT: B 392 ASP cc_start: 0.7944 (t0) cc_final: 0.7718 (t0) REVERT: B 421 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7247 (ptm-80) REVERT: B 451 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7609 (m-10) outliers start: 27 outliers final: 12 residues processed: 89 average time/residue: 0.8501 time to fit residues: 82.2512 Evaluate side-chains 80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 55.1659 > 50: distance: 2 - 18: 21.809 distance: 6 - 22: 15.052 distance: 10 - 27: 6.605 distance: 15 - 18: 24.891 distance: 18 - 19: 18.836 distance: 19 - 20: 17.206 distance: 20 - 21: 23.880 distance: 20 - 22: 27.952 distance: 21 - 41: 12.231 distance: 22 - 23: 18.284 distance: 23 - 24: 10.674 distance: 23 - 26: 13.536 distance: 24 - 25: 23.614 distance: 24 - 27: 14.592 distance: 25 - 49: 27.226 distance: 27 - 28: 3.416 distance: 28 - 29: 9.128 distance: 28 - 31: 7.158 distance: 29 - 30: 7.016 distance: 29 - 34: 11.432 distance: 30 - 57: 17.161 distance: 31 - 32: 10.902 distance: 31 - 33: 13.627 distance: 34 - 35: 15.425 distance: 35 - 36: 14.628 distance: 35 - 38: 14.391 distance: 36 - 37: 17.579 distance: 36 - 41: 5.421 distance: 38 - 39: 11.627 distance: 38 - 40: 16.191 distance: 41 - 42: 9.466 distance: 42 - 43: 29.418 distance: 42 - 45: 11.381 distance: 43 - 44: 17.616 distance: 43 - 49: 28.500 distance: 45 - 46: 16.405 distance: 45 - 47: 17.225 distance: 46 - 48: 10.950 distance: 49 - 50: 12.115 distance: 50 - 51: 13.645 distance: 50 - 53: 9.485 distance: 51 - 52: 27.883 distance: 51 - 57: 11.196 distance: 53 - 54: 26.832 distance: 53 - 55: 13.199 distance: 54 - 56: 23.427 distance: 57 - 58: 21.731 distance: 58 - 59: 25.471 distance: 58 - 61: 31.814 distance: 59 - 60: 20.098 distance: 59 - 64: 26.601 distance: 61 - 62: 25.814 distance: 61 - 63: 37.050 distance: 64 - 65: 16.141 distance: 65 - 66: 21.616 distance: 65 - 68: 25.786 distance: 66 - 67: 7.989 distance: 66 - 75: 23.524 distance: 68 - 69: 16.081 distance: 69 - 70: 10.440 distance: 70 - 71: 10.603 distance: 71 - 72: 3.955 distance: 75 - 76: 33.649 distance: 76 - 77: 21.933 distance: 76 - 79: 55.166 distance: 77 - 80: 28.826 distance: 80 - 81: 13.830 distance: 80 - 86: 24.936 distance: 81 - 82: 17.032 distance: 81 - 84: 15.071 distance: 82 - 83: 10.294 distance: 82 - 87: 6.974 distance: 84 - 85: 25.057 distance: 85 - 86: 29.417