Starting phenix.real_space_refine on Tue Jan 14 11:43:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo9_33341/01_2025/7xo9_33341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo9_33341/01_2025/7xo9_33341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo9_33341/01_2025/7xo9_33341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo9_33341/01_2025/7xo9_33341.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo9_33341/01_2025/7xo9_33341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo9_33341/01_2025/7xo9_33341.cif" } resolution = 3.0 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4154 2.51 5 N 1074 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6483 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1582 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.73, per 1000 atoms: 0.88 Number of scatterers: 6483 At special positions: 0 Unit cell: (97.232, 70.864, 117.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1216 8.00 N 1074 7.00 C 4154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 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 NAG-ASN " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 90 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 956.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 55.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.606A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.776A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.653A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.617A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.002A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.616A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.649A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.956A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.750A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.867A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 531 removed outlier: 3.542A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.743A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.597A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.540A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.602A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.645A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.073A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.027A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 846 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: 1.49 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2040 1.34 - 1.45: 1106 1.45 - 1.57: 3462 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6666 Sorted by residual: bond pdb=" N ASN D 322 " pdb=" CA ASN D 322 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.31e-02 5.83e+03 4.65e+00 bond pdb=" N SER D 19 " pdb=" CA SER D 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" C3 NAG D 904 " pdb=" O3 NAG D 904 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C3 NAG D 905 " pdb=" O3 NAG D 905 " ideal model delta sigma weight residual 1.403 1.429 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 6661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8884 1.33 - 2.65: 112 2.65 - 3.98: 53 3.98 - 5.31: 9 5.31 - 6.63: 2 Bond angle restraints: 9060 Sorted by residual: angle pdb=" C ASN D 322 " pdb=" CA ASN D 322 " pdb=" CB ASN D 322 " ideal model delta sigma weight residual 109.76 116.39 -6.63 1.99e+00 2.53e-01 1.11e+01 angle pdb=" C ASN D 322 " pdb=" N MET D 323 " pdb=" CA MET D 323 " ideal model delta sigma weight residual 120.87 126.40 -5.53 1.69e+00 3.50e-01 1.07e+01 angle pdb=" CA ASN D 322 " pdb=" C ASN D 322 " pdb=" O ASN D 322 " ideal model delta sigma weight residual 121.81 118.90 2.91 1.18e+00 7.18e-01 6.09e+00 angle pdb=" N ILE D 544 " pdb=" CA ILE D 544 " pdb=" C ILE D 544 " ideal model delta sigma weight residual 112.98 110.04 2.94 1.25e+00 6.40e-01 5.53e+00 angle pdb=" O PRO D 321 " pdb=" C PRO D 321 " pdb=" N ASN D 322 " ideal model delta sigma weight residual 123.06 120.18 2.88 1.23e+00 6.61e-01 5.48e+00 ... (remaining 9055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3643 17.84 - 35.69: 249 35.69 - 53.53: 43 53.53 - 71.37: 13 71.37 - 89.22: 6 Dihedral angle restraints: 3954 sinusoidal: 1626 harmonic: 2328 Sorted by residual: dihedral pdb=" CA LYS D 68 " pdb=" CB LYS D 68 " pdb=" CG LYS D 68 " pdb=" CD LYS D 68 " ideal model delta sinusoidal sigma weight residual 180.00 120.09 59.91 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS D 341 " pdb=" CA LYS D 341 " pdb=" CB LYS D 341 " pdb=" CG LYS D 341 " ideal model delta sinusoidal sigma weight residual -180.00 -121.74 -58.26 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET D 323 " pdb=" CG MET D 323 " pdb=" SD MET D 323 " pdb=" CE MET D 323 " ideal model delta sinusoidal sigma weight residual 180.00 122.17 57.83 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 952 0.249 - 0.498: 0 0.498 - 0.747: 0 0.747 - 0.995: 0 0.995 - 1.244: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" C1 NAG D 905 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 905 " pdb=" O5 NAG D 905 " both_signs ideal model delta sigma weight residual False -2.40 -1.16 -1.24 2.00e-01 2.50e+01 3.87e+01 chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN D 322 " pdb=" N ASN D 322 " pdb=" C ASN D 322 " pdb=" CB ASN D 322 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 950 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 905 " 0.245 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C7 NAG D 905 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 905 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG D 905 " -0.349 2.00e-02 2.50e+03 pdb=" O7 NAG D 905 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 903 " -0.247 2.00e-02 2.50e+03 2.08e-01 5.43e+02 pdb=" C7 NAG D 903 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG D 903 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG D 903 " 0.353 2.00e-02 2.50e+03 pdb=" O7 NAG D 903 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 904 " 0.054 2.00e-02 2.50e+03 4.46e-02 2.48e+01 pdb=" C7 NAG D 904 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG D 904 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG D 904 " -0.070 2.00e-02 2.50e+03 pdb=" O7 NAG D 904 " -0.009 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 75 2.63 - 3.20: 6069 3.20 - 3.76: 10152 3.76 - 4.33: 14209 4.33 - 4.90: 23577 Nonbonded interactions: 54082 Sorted by model distance: nonbonded pdb=" O ALA D 501 " pdb=" OG SER D 507 " model vdw 2.059 3.040 nonbonded pdb=" O GLN D 388 " pdb=" NH1 ARG D 393 " model vdw 2.184 3.120 nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 902 " model vdw 2.186 2.230 nonbonded pdb=" O TYR D 515 " pdb=" OG1 THR D 519 " model vdw 2.249 3.040 nonbonded pdb=" OG SER D 331 " pdb=" O ILE D 358 " model vdw 2.250 3.040 ... (remaining 54077 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: 6.470 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.960 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6666 Z= 0.148 Angle : 0.472 6.634 9060 Z= 0.252 Chirality : 0.056 1.244 953 Planarity : 0.009 0.210 1172 Dihedral : 13.058 89.215 2457 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % 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: -1.79 (0.27), residues: 789 helix: -0.48 (0.24), residues: 396 sheet: -1.57 (0.71), residues: 45 loop : -1.92 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 165 HIS 0.001 0.000 HIS D 535 PHE 0.005 0.001 PHE A 515 TYR 0.007 0.001 TYR A 369 ARG 0.002 0.000 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8069 (p0) cc_final: 0.7819 (p0) REVERT: D 37 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6286 (mt-10) REVERT: D 94 LYS cc_start: 0.7854 (tttt) cc_final: 0.7561 (ttpp) REVERT: D 270 MET cc_start: 0.7896 (tpp) cc_final: 0.7637 (tpt) REVERT: D 294 THR cc_start: 0.6608 (p) cc_final: 0.6075 (p) REVERT: D 295 ASP cc_start: 0.6696 (p0) cc_final: 0.6268 (t0) REVERT: D 556 ASN cc_start: 0.7117 (m-40) cc_final: 0.6900 (m-40) REVERT: D 589 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6439 (tp30) REVERT: D 613 TYR cc_start: 0.6279 (p90) cc_final: 0.5932 (p90) outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 1.2137 time to fit residues: 254.7410 Evaluate side-chains 150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 31 optimal weight: 0.0470 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 0.0060 chunk 70 optimal weight: 0.0970 overall best weight: 0.1292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 437 ASN A 439 ASN A 448 ASN A 460 ASN A 474 GLN A 481 ASN D 51 ASN D 96 GLN D 101 GLN D 149 ASN D 300 GLN D 373 HIS D 505 HIS D 522 GLN D 524 GLN D 578 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127537 restraints weight = 9168.244| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.00 r_work: 0.3588 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6666 Z= 0.180 Angle : 0.543 9.622 9060 Z= 0.277 Chirality : 0.041 0.130 953 Planarity : 0.004 0.036 1172 Dihedral : 3.663 28.983 929 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.02 % Allowed : 19.54 % Favored : 77.44 % 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: -0.52 (0.29), residues: 789 helix: 0.42 (0.26), residues: 403 sheet: -0.83 (0.78), residues: 45 loop : -1.15 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 203 HIS 0.005 0.001 HIS D 374 PHE 0.023 0.002 PHE D 555 TYR 0.019 0.001 TYR A 369 ARG 0.006 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.3738 (OUTLIER) cc_final: 0.3256 (p0) REVERT: A 405 ASN cc_start: 0.8556 (p0) cc_final: 0.8239 (p0) REVERT: D 37 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7008 (mt-10) REVERT: D 295 ASP cc_start: 0.6854 (p0) cc_final: 0.6457 (t0) REVERT: D 347 THR cc_start: 0.7973 (m) cc_final: 0.7690 (p) REVERT: D 363 LYS cc_start: 0.7772 (mptp) cc_final: 0.7519 (mptp) REVERT: D 518 ARG cc_start: 0.8355 (tmm160) cc_final: 0.8051 (ttp80) REVERT: D 555 PHE cc_start: 0.8357 (t80) cc_final: 0.7975 (t80) REVERT: D 556 ASN cc_start: 0.8153 (m-40) cc_final: 0.7653 (m-40) REVERT: D 613 TYR cc_start: 0.6856 (p90) cc_final: 0.6398 (p90) outliers start: 21 outliers final: 8 residues processed: 172 average time/residue: 1.1945 time to fit residues: 215.7811 Evaluate side-chains 152 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.0050 chunk 41 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 239 HIS D 300 GLN D 345 HIS D 373 HIS D 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125252 restraints weight = 9352.621| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.04 r_work: 0.3511 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6666 Z= 0.234 Angle : 0.548 7.960 9060 Z= 0.278 Chirality : 0.042 0.133 953 Planarity : 0.004 0.037 1172 Dihedral : 3.701 19.842 925 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.02 % Allowed : 20.40 % Favored : 76.58 % 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: -0.20 (0.30), residues: 789 helix: 0.67 (0.26), residues: 404 sheet: -0.76 (0.75), residues: 45 loop : -0.96 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 349 HIS 0.006 0.001 HIS D 374 PHE 0.014 0.002 PHE D 555 TYR 0.016 0.001 TYR A 369 ARG 0.005 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8493 (p0) cc_final: 0.8215 (p0) REVERT: A 408 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8235 (m) REVERT: D 101 GLN cc_start: 0.7637 (tt0) cc_final: 0.7426 (tt0) REVERT: D 114 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7569 (mmmt) REVERT: D 295 ASP cc_start: 0.6998 (p0) cc_final: 0.6739 (t0) REVERT: D 347 THR cc_start: 0.8108 (m) cc_final: 0.7885 (p) REVERT: D 518 ARG cc_start: 0.8352 (tmm160) cc_final: 0.7994 (ppt90) REVERT: D 541 LYS cc_start: 0.7541 (mttm) cc_final: 0.7333 (mttp) REVERT: D 555 PHE cc_start: 0.8453 (t80) cc_final: 0.8249 (t80) REVERT: D 556 ASN cc_start: 0.8125 (m-40) cc_final: 0.7783 (m110) REVERT: D 613 TYR cc_start: 0.7239 (p90) cc_final: 0.6686 (p90) outliers start: 21 outliers final: 8 residues processed: 166 average time/residue: 1.1945 time to fit residues: 208.7044 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 477 ASN D 81 GLN D 330 ASN D 578 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121585 restraints weight = 9332.868| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.02 r_work: 0.3448 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 6666 Z= 0.367 Angle : 0.619 11.077 9060 Z= 0.313 Chirality : 0.045 0.140 953 Planarity : 0.005 0.048 1172 Dihedral : 4.172 21.089 925 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.03 % Allowed : 19.68 % Favored : 75.29 % 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: -0.27 (0.30), residues: 789 helix: 0.65 (0.26), residues: 400 sheet: -0.86 (0.72), residues: 43 loop : -1.04 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 349 HIS 0.008 0.001 HIS D 374 PHE 0.018 0.002 PHE D 603 TYR 0.021 0.002 TYR D 50 ARG 0.004 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8378 (p0) cc_final: 0.8168 (p0) REVERT: A 408 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8285 (m) REVERT: D 37 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7325 (mp0) REVERT: D 114 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7530 (mmmt) REVERT: D 249 MET cc_start: 0.7875 (mmm) cc_final: 0.7674 (mmt) REVERT: D 406 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 518 ARG cc_start: 0.8321 (tmm160) cc_final: 0.7977 (ttp80) REVERT: D 556 ASN cc_start: 0.8239 (m-40) cc_final: 0.7717 (m110) REVERT: D 613 TYR cc_start: 0.7573 (p90) cc_final: 0.7037 (p90) outliers start: 35 outliers final: 15 residues processed: 177 average time/residue: 1.2658 time to fit residues: 235.2745 Evaluate side-chains 160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 470 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 8 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 overall best weight: 0.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 210 ASN D 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123350 restraints weight = 9245.930| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.01 r_work: 0.3477 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6666 Z= 0.199 Angle : 0.527 7.583 9060 Z= 0.269 Chirality : 0.041 0.130 953 Planarity : 0.004 0.041 1172 Dihedral : 3.795 16.315 925 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.30 % Allowed : 21.12 % Favored : 75.57 % 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: -0.01 (0.30), residues: 789 helix: 0.88 (0.27), residues: 399 sheet: -0.74 (0.73), residues: 43 loop : -0.92 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.020 0.001 PHE D 285 TYR 0.017 0.001 TYR A 369 ARG 0.004 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8423 (p0) cc_final: 0.8131 (p0) REVERT: D 43 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8630 (p) REVERT: D 114 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7647 (mmmm) REVERT: D 249 MET cc_start: 0.7814 (mmm) cc_final: 0.7576 (mmm) REVERT: D 257 SER cc_start: 0.8592 (t) cc_final: 0.8285 (p) REVERT: D 363 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7730 (mmtt) REVERT: D 406 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 470 LYS cc_start: 0.8396 (tppp) cc_final: 0.8172 (tttt) REVERT: D 518 ARG cc_start: 0.8342 (tmm160) cc_final: 0.8047 (ttp80) REVERT: D 556 ASN cc_start: 0.8215 (m-40) cc_final: 0.7698 (m110) REVERT: D 577 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8061 (mtpp) REVERT: D 613 TYR cc_start: 0.7552 (p90) cc_final: 0.7074 (p90) outliers start: 23 outliers final: 10 residues processed: 162 average time/residue: 1.2919 time to fit residues: 219.2918 Evaluate side-chains 152 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 0.0070 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 56 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 23 optimal weight: 0.9990 overall best weight: 0.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 287 GLN D 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123850 restraints weight = 9192.978| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.99 r_work: 0.3489 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6666 Z= 0.180 Angle : 0.510 5.960 9060 Z= 0.261 Chirality : 0.041 0.128 953 Planarity : 0.004 0.042 1172 Dihedral : 3.665 14.107 925 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.73 % Allowed : 22.56 % Favored : 74.71 % 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: 0.18 (0.30), residues: 789 helix: 1.05 (0.27), residues: 399 sheet: -0.54 (0.74), residues: 43 loop : -0.85 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.023 0.001 PHE D 285 TYR 0.017 0.001 TYR A 369 ARG 0.004 0.000 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 CYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6772 (m) REVERT: A 405 ASN cc_start: 0.8415 (p0) cc_final: 0.8107 (p0) REVERT: D 37 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7251 (mp0) REVERT: D 43 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8652 (p) REVERT: D 114 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7545 (mmmm) REVERT: D 249 MET cc_start: 0.7801 (mmm) cc_final: 0.7528 (mmm) REVERT: D 257 SER cc_start: 0.8515 (t) cc_final: 0.8273 (p) REVERT: D 349 TRP cc_start: 0.8569 (m100) cc_final: 0.8245 (m100) REVERT: D 363 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7684 (mmtt) REVERT: D 406 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7537 (mm-30) REVERT: D 518 ARG cc_start: 0.8342 (tmm160) cc_final: 0.8066 (ttp80) REVERT: D 531 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: D 556 ASN cc_start: 0.8229 (m-40) cc_final: 0.7735 (m110) REVERT: D 577 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8064 (mtpp) REVERT: D 613 TYR cc_start: 0.7603 (p90) cc_final: 0.7017 (p90) outliers start: 19 outliers final: 8 residues processed: 163 average time/residue: 1.1836 time to fit residues: 203.0735 Evaluate side-chains 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 48 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 0.0370 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 378 HIS D 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124786 restraints weight = 9227.024| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.00 r_work: 0.3487 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6666 Z= 0.161 Angle : 0.500 5.805 9060 Z= 0.256 Chirality : 0.040 0.128 953 Planarity : 0.004 0.042 1172 Dihedral : 3.544 13.192 925 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.44 % Allowed : 23.28 % Favored : 74.28 % 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: 0.36 (0.30), residues: 789 helix: 1.20 (0.27), residues: 399 sheet: -0.38 (0.75), residues: 43 loop : -0.78 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.024 0.001 PHE D 285 TYR 0.022 0.001 TYR D 50 ARG 0.009 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8407 (p0) cc_final: 0.8085 (p0) REVERT: D 37 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7225 (mt-10) REVERT: D 43 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8678 (p) REVERT: D 114 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7540 (mmmm) REVERT: D 249 MET cc_start: 0.7759 (mmm) cc_final: 0.7469 (mmm) REVERT: D 257 SER cc_start: 0.8479 (t) cc_final: 0.8265 (p) REVERT: D 363 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7600 (mmtt) REVERT: D 406 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7574 (mm-30) REVERT: D 518 ARG cc_start: 0.8337 (tmm160) cc_final: 0.8069 (ttp80) REVERT: D 556 ASN cc_start: 0.8221 (m-40) cc_final: 0.7730 (m110) REVERT: D 558 LEU cc_start: 0.7804 (mt) cc_final: 0.7595 (mp) REVERT: D 577 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8064 (mtpp) REVERT: D 613 TYR cc_start: 0.7594 (p90) cc_final: 0.7075 (p90) outliers start: 17 outliers final: 8 residues processed: 160 average time/residue: 1.3505 time to fit residues: 228.2935 Evaluate side-chains 159 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 29 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.0370 chunk 77 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 overall best weight: 0.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126774 restraints weight = 9192.524| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.03 r_work: 0.3513 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6666 Z= 0.142 Angle : 0.495 5.647 9060 Z= 0.254 Chirality : 0.040 0.127 953 Planarity : 0.004 0.042 1172 Dihedral : 3.423 12.430 925 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.44 % Allowed : 23.56 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 789 helix: 1.31 (0.27), residues: 399 sheet: -0.35 (0.75), residues: 43 loop : -0.69 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 168 HIS 0.004 0.000 HIS D 374 PHE 0.021 0.001 PHE D 285 TYR 0.018 0.001 TYR D 50 ARG 0.008 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 CYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6732 (m) REVERT: A 405 ASN cc_start: 0.8408 (p0) cc_final: 0.8081 (p0) REVERT: D 37 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7215 (mt-10) REVERT: D 114 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7515 (mmmm) REVERT: D 117 ASN cc_start: 0.8234 (m-40) cc_final: 0.8010 (m-40) REVERT: D 249 MET cc_start: 0.7664 (mmm) cc_final: 0.7424 (mmm) REVERT: D 270 MET cc_start: 0.8311 (tpp) cc_final: 0.8013 (tpp) REVERT: D 388 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7337 (mm-40) REVERT: D 406 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 518 ARG cc_start: 0.8305 (tmm160) cc_final: 0.8054 (ttp80) REVERT: D 531 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: D 556 ASN cc_start: 0.8167 (m-40) cc_final: 0.7724 (m-40) REVERT: D 577 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7993 (mtpp) REVERT: D 613 TYR cc_start: 0.7542 (p90) cc_final: 0.7009 (p90) outliers start: 17 outliers final: 9 residues processed: 167 average time/residue: 1.1455 time to fit residues: 202.2559 Evaluate side-chains 161 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 69.3338 > 50: distance: 13 - 33: 10.286 distance: 25 - 33: 13.888 distance: 33 - 34: 16.431 distance: 34 - 35: 11.647 distance: 34 - 37: 4.617 distance: 35 - 36: 44.280 distance: 35 - 41: 19.839 distance: 37 - 38: 17.632 distance: 38 - 39: 26.541 distance: 38 - 40: 19.462 distance: 41 - 42: 20.319 distance: 42 - 43: 17.655 distance: 42 - 45: 42.611 distance: 43 - 44: 15.228 distance: 43 - 52: 40.888 distance: 45 - 46: 13.771 distance: 46 - 47: 30.799 distance: 46 - 48: 16.610 distance: 47 - 49: 18.757 distance: 48 - 50: 11.175 distance: 49 - 51: 16.251 distance: 50 - 51: 30.205 distance: 52 - 53: 41.325 distance: 53 - 54: 19.147 distance: 53 - 56: 44.462 distance: 54 - 55: 35.299 distance: 54 - 57: 10.311 distance: 57 - 58: 32.604 distance: 57 - 63: 15.036 distance: 58 - 59: 15.579 distance: 58 - 61: 4.958 distance: 59 - 60: 40.562 distance: 59 - 64: 18.818 distance: 61 - 62: 27.670 distance: 62 - 63: 41.579 distance: 64 - 65: 5.114 distance: 65 - 66: 28.798 distance: 65 - 68: 41.022 distance: 66 - 67: 4.452 distance: 66 - 75: 56.955 distance: 68 - 69: 17.882 distance: 69 - 70: 38.461 distance: 69 - 71: 12.733 distance: 70 - 72: 30.203 distance: 71 - 73: 34.636 distance: 72 - 74: 12.699 distance: 73 - 74: 47.936 distance: 76 - 77: 40.787 distance: 77 - 86: 3.665 distance: 79 - 80: 37.038 distance: 80 - 81: 9.032 distance: 80 - 82: 20.087 distance: 81 - 83: 28.024 distance: 83 - 85: 37.247 distance: 84 - 85: 37.226 distance: 86 - 87: 19.968 distance: 86 - 165: 33.771 distance: 87 - 88: 25.537 distance: 87 - 90: 28.637 distance: 88 - 89: 29.693 distance: 88 - 91: 5.788 distance: 89 - 162: 30.886 distance: 91 - 92: 20.498 distance: 92 - 93: 23.441 distance: 92 - 95: 20.412 distance: 93 - 94: 6.225 distance: 93 - 102: 28.943 distance: 95 - 96: 19.481 distance: 96 - 97: 38.379 distance: 96 - 98: 52.860 distance: 97 - 99: 45.235 distance: 98 - 100: 7.913 distance: 99 - 101: 30.723 distance: 100 - 101: 32.724 distance: 102 - 103: 37.113 distance: 102 - 152: 25.471 distance: 103 - 104: 43.452 distance: 103 - 106: 12.343 distance: 104 - 105: 51.196 distance: 105 - 149: 31.932 distance: 106 - 107: 18.431 distance: 107 - 108: 12.826 distance: 108 - 109: 43.010 distance: 109 - 110: 37.558 distance: 111 - 112: 34.067 distance: 112 - 113: 12.218 distance: 112 - 115: 44.993 distance: 113 - 117: 35.013