Starting phenix.real_space_refine on Tue Jan 14 04:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugv_26497/01_2025/7ugv_26497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugv_26497/01_2025/7ugv_26497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ugv_26497/01_2025/7ugv_26497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugv_26497/01_2025/7ugv_26497.map" model { file = "/net/cci-nas-00/data/ceres_data/7ugv_26497/01_2025/7ugv_26497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugv_26497/01_2025/7ugv_26497.cif" } resolution = 2.94 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= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2846 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 16 5.16 5 Na 3 4.78 5 C 2038 2.51 5 N 506 2.21 5 O 543 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3107 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3104 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.21, per 1000 atoms: 1.03 Number of scatterers: 3107 At special positions: 0 Unit cell: (69.012, 74.976, 74.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 Na 3 11.00 F 1 9.00 O 543 8.00 N 506 7.00 C 2038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 462.9 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 4.147A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 32 Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.803A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.555A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 108 removed outlier: 3.597A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.661A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.519A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.504A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.519A pdb=" N HIS A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 246 removed outlier: 4.081A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 277 through 292 Proline residue: A 283 - end of helix removed outlier: 3.517A pdb=" N ALA A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 301 through 310 removed outlier: 4.173A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.624A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.604A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.323A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.811A pdb=" N EFC A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 417 removed outlier: 3.554A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 696 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: 0.86 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 986 1.37 - 1.55: 2147 1.55 - 1.73: 1 1.73 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3165 Sorted by residual: bond pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 8.97e+00 bond pdb=" N LEU A 305 " pdb=" CA LEU A 305 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.20e+00 bond pdb=" N ASP A 312 " pdb=" CA ASP A 312 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 bond pdb=" N LEU A 316 " pdb=" CA LEU A 316 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.72e+00 bond pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.65e+00 ... (remaining 3160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 4212 1.72 - 3.43: 88 3.43 - 5.15: 11 5.15 - 6.87: 3 6.87 - 8.58: 1 Bond angle restraints: 4315 Sorted by residual: angle pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" O ILE A 309 " ideal model delta sigma weight residual 120.95 117.68 3.27 1.04e+00 9.25e-01 9.87e+00 angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 110.23 -8.58 3.00e+00 1.11e-01 8.19e+00 angle pdb=" N LEU A 316 " pdb=" CA LEU A 316 " pdb=" C LEU A 316 " ideal model delta sigma weight residual 111.28 108.43 2.85 1.09e+00 8.42e-01 6.83e+00 angle pdb=" CA ALA A 307 " pdb=" C ALA A 307 " pdb=" O ALA A 307 " ideal model delta sigma weight residual 120.55 117.93 2.62 1.06e+00 8.90e-01 6.10e+00 angle pdb=" O GLY A 313 " pdb=" C GLY A 313 " pdb=" N THR A 314 " ideal model delta sigma weight residual 122.19 124.55 -2.36 9.60e-01 1.09e+00 6.04e+00 ... (remaining 4310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 1773 15.18 - 30.36: 64 30.36 - 45.54: 11 45.54 - 60.73: 2 60.73 - 75.91: 3 Dihedral angle restraints: 1853 sinusoidal: 670 harmonic: 1183 Sorted by residual: dihedral pdb=" CB MET A 362 " pdb=" CG MET A 362 " pdb=" SD MET A 362 " pdb=" CE MET A 362 " ideal model delta sinusoidal sigma weight residual 60.00 102.25 -42.25 3 1.50e+01 4.44e-03 7.58e+00 dihedral pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" CB LEU A 91 " pdb=" CG LEU A 91 " ideal model delta sinusoidal sigma weight residual -60.00 -94.69 34.69 3 1.50e+01 4.44e-03 5.89e+00 dihedral pdb=" N LEU A 78 " pdb=" CA LEU A 78 " pdb=" CB LEU A 78 " pdb=" CG LEU A 78 " ideal model delta sinusoidal sigma weight residual -180.00 -145.57 -34.43 3 1.50e+01 4.44e-03 5.83e+00 ... (remaining 1850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 368 0.034 - 0.068: 134 0.068 - 0.101: 29 0.101 - 0.135: 7 0.135 - 0.169: 2 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA LEU A 305 " pdb=" N LEU A 305 " pdb=" C LEU A 305 " pdb=" CB LEU A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA LEU A 316 " pdb=" N LEU A 316 " pdb=" C LEU A 316 " pdb=" CB LEU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA MET A 311 " pdb=" N MET A 311 " pdb=" C MET A 311 " pdb=" CB MET A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 537 not shown) Planarity restraints: 532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 377 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO A 206 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 10 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO A 11 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " -0.015 5.00e-02 4.00e+02 ... (remaining 529 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 31 2.67 - 3.23: 3207 3.23 - 3.78: 4555 3.78 - 4.34: 6229 4.34 - 4.90: 10179 Nonbonded interactions: 24201 Sorted by model distance: nonbonded pdb=" O ASN A 310 " pdb="NA NA A 502 " model vdw 2.111 2.470 nonbonded pdb=" O THR A 308 " pdb="NA NA A 503 " model vdw 2.229 2.470 nonbonded pdb=" OD1 ASP A 312 " pdb="NA NA A 504 " model vdw 2.238 2.470 nonbonded pdb=" N GLY A 359 " pdb=" OD2 ASP A 501 " model vdw 2.377 3.120 nonbonded pdb=" O ALA A 348 " pdb=" OG1 THR A 352 " model vdw 2.389 3.040 ... (remaining 24196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.003 0.047 3165 Z= 0.223 Angle : 0.566 8.583 4315 Z= 0.326 Chirality : 0.039 0.169 540 Planarity : 0.004 0.030 532 Dihedral : 9.131 75.906 1103 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.40), residues: 412 helix: 1.83 (0.27), residues: 328 sheet: None (None), residues: 0 loop : 0.64 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.006 0.001 PHE A 122 TYR 0.017 0.001 TYR A 89 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.367 Fit side-chains REVERT: A 5 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7573 (mmt-90) REVERT: A 121 GLN cc_start: 0.9068 (mt0) cc_final: 0.8747 (mt0) REVERT: A 291 GLU cc_start: 0.8584 (mp0) cc_final: 0.8340 (mp0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.3645 time to fit residues: 79.7554 Evaluate side-chains 40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.067146 restraints weight = 6010.271| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.59 r_work: 0.2743 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3165 Z= 0.224 Angle : 0.601 7.802 4315 Z= 0.315 Chirality : 0.040 0.134 540 Planarity : 0.005 0.039 532 Dihedral : 4.487 44.918 445 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.78 % Allowed : 9.88 % Favored : 87.35 % 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: 3.23 (0.41), residues: 412 helix: 2.39 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 1.15 (0.76), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.010 0.002 PHE A 156 TYR 0.020 0.002 TYR A 299 ARG 0.004 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.333 Fit side-chains REVERT: A 5 ARG cc_start: 0.7460 (mmt90) cc_final: 0.6586 (mmt-90) REVERT: A 9 GLU cc_start: 0.8557 (mp0) cc_final: 0.7828 (mp0) REVERT: A 125 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8702 (t-90) REVERT: A 291 GLU cc_start: 0.8666 (mp0) cc_final: 0.8385 (mp0) REVERT: A 296 GLU cc_start: 0.9073 (tp30) cc_final: 0.8733 (tp30) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 1.3863 time to fit residues: 61.4243 Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.092536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.065681 restraints weight = 6086.295| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.58 r_work: 0.2718 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3165 Z= 0.217 Angle : 0.531 8.015 4315 Z= 0.276 Chirality : 0.038 0.135 540 Planarity : 0.004 0.035 532 Dihedral : 4.157 35.373 445 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 10.80 % Favored : 86.42 % 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: 3.45 (0.41), residues: 412 helix: 2.59 (0.28), residues: 331 sheet: None (None), residues: 0 loop : 1.03 (0.74), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.011 0.001 PHE A 50 TYR 0.016 0.002 TYR A 299 ARG 0.005 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.345 Fit side-chains REVERT: A 5 ARG cc_start: 0.7589 (mmt90) cc_final: 0.6790 (mmt-90) REVERT: A 9 GLU cc_start: 0.8532 (mp0) cc_final: 0.7802 (mp0) REVERT: A 125 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8646 (t-90) REVERT: A 291 GLU cc_start: 0.8672 (mp0) cc_final: 0.8316 (mp0) REVERT: A 296 GLU cc_start: 0.8935 (tp30) cc_final: 0.8693 (tp30) REVERT: A 318 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7201 (mt0) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 1.4938 time to fit residues: 59.9122 Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 374 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.092352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.065254 restraints weight = 6080.476| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.62 r_work: 0.2701 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3165 Z= 0.236 Angle : 0.532 8.404 4315 Z= 0.274 Chirality : 0.038 0.120 540 Planarity : 0.004 0.035 532 Dihedral : 4.061 27.906 445 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.16 % Allowed : 11.73 % Favored : 86.11 % 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: 3.46 (0.41), residues: 412 helix: 2.58 (0.28), residues: 337 sheet: None (None), residues: 0 loop : 1.03 (0.78), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.011 0.001 PHE A 301 TYR 0.016 0.002 TYR A 299 ARG 0.005 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.334 Fit side-chains REVERT: A 5 ARG cc_start: 0.7615 (mmt90) cc_final: 0.6851 (mmt-90) REVERT: A 9 GLU cc_start: 0.8563 (mp0) cc_final: 0.7838 (mp0) REVERT: A 291 GLU cc_start: 0.8676 (mp0) cc_final: 0.8279 (mp0) REVERT: A 296 GLU cc_start: 0.8976 (tp30) cc_final: 0.8713 (tp30) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 1.5197 time to fit residues: 56.1506 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 374 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.065646 restraints weight = 6123.928| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.62 r_work: 0.2715 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3165 Z= 0.204 Angle : 0.528 8.757 4315 Z= 0.266 Chirality : 0.038 0.120 540 Planarity : 0.004 0.034 532 Dihedral : 4.013 28.478 445 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.47 % Allowed : 11.42 % Favored : 86.11 % 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: 3.40 (0.41), residues: 412 helix: 2.60 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.59 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.010 0.001 PHE A 301 TYR 0.014 0.001 TYR A 299 ARG 0.005 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.333 Fit side-chains REVERT: A 5 ARG cc_start: 0.7594 (mmt90) cc_final: 0.6829 (mmt-90) REVERT: A 9 GLU cc_start: 0.8485 (mp0) cc_final: 0.7766 (mp0) REVERT: A 120 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8528 (tp-100) REVERT: A 291 GLU cc_start: 0.8727 (mp0) cc_final: 0.8388 (mp0) REVERT: A 296 GLU cc_start: 0.8965 (tp30) cc_final: 0.8697 (tp30) outliers start: 8 outliers final: 5 residues processed: 38 average time/residue: 1.5391 time to fit residues: 60.0531 Evaluate side-chains 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 374 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.065367 restraints weight = 6161.945| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.64 r_work: 0.2709 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3165 Z= 0.215 Angle : 0.543 8.965 4315 Z= 0.271 Chirality : 0.038 0.120 540 Planarity : 0.004 0.034 532 Dihedral : 4.000 28.032 445 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.09 % Allowed : 11.73 % Favored : 85.19 % 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: 3.42 (0.41), residues: 412 helix: 2.60 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.65 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.010 0.001 PHE A 301 TYR 0.014 0.001 TYR A 299 ARG 0.006 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.362 Fit side-chains REVERT: A 5 ARG cc_start: 0.7643 (mmt90) cc_final: 0.6949 (mmt-90) REVERT: A 9 GLU cc_start: 0.8413 (mp0) cc_final: 0.7689 (mp0) REVERT: A 120 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8547 (tp-100) REVERT: A 291 GLU cc_start: 0.8730 (mp0) cc_final: 0.8374 (mp0) REVERT: A 296 GLU cc_start: 0.8939 (tp30) cc_final: 0.8656 (tp30) outliers start: 10 outliers final: 5 residues processed: 38 average time/residue: 1.6033 time to fit residues: 62.5015 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 69.1994 > 50: distance: 15 - 20: 7.011 distance: 20 - 21: 12.869 distance: 21 - 22: 6.323 distance: 21 - 24: 6.653 distance: 22 - 23: 5.332 distance: 22 - 28: 4.826 distance: 23 - 50: 17.710 distance: 24 - 25: 14.560 distance: 25 - 26: 6.322 distance: 25 - 27: 7.733 distance: 28 - 29: 8.573 distance: 28 - 34: 10.357 distance: 29 - 30: 5.458 distance: 29 - 32: 3.304 distance: 30 - 31: 6.801 distance: 30 - 35: 8.447 distance: 32 - 33: 8.707 distance: 33 - 34: 8.110 distance: 35 - 36: 4.722 distance: 36 - 37: 3.241 distance: 36 - 39: 5.812 distance: 37 - 38: 4.967 distance: 37 - 46: 6.434 distance: 38 - 63: 32.394 distance: 39 - 40: 3.604 distance: 40 - 41: 3.586 distance: 40 - 42: 3.877 distance: 41 - 43: 7.380 distance: 43 - 45: 5.645 distance: 44 - 45: 5.585 distance: 46 - 47: 9.573 distance: 47 - 48: 9.794 distance: 48 - 49: 6.777 distance: 48 - 50: 7.040 distance: 49 - 68: 18.746 distance: 50 - 51: 5.050 distance: 51 - 54: 18.242 distance: 52 - 53: 6.344 distance: 52 - 55: 7.971 distance: 53 - 76: 21.802 distance: 55 - 56: 18.980 distance: 56 - 59: 17.938 distance: 57 - 58: 30.298 distance: 57 - 63: 40.221 distance: 59 - 60: 10.330 distance: 60 - 61: 25.060 distance: 60 - 62: 21.814 distance: 63 - 64: 37.151 distance: 64 - 65: 22.520 distance: 64 - 67: 7.419 distance: 65 - 66: 16.978 distance: 65 - 68: 42.252 distance: 68 - 69: 15.409 distance: 69 - 70: 12.328 distance: 69 - 72: 10.789 distance: 70 - 71: 16.047 distance: 70 - 76: 13.732 distance: 72 - 73: 19.078 distance: 73 - 74: 11.280 distance: 73 - 75: 13.348 distance: 76 - 77: 23.788 distance: 77 - 78: 12.280 distance: 78 - 79: 8.229 distance: 78 - 80: 13.977 distance: 80 - 81: 19.522 distance: 81 - 82: 7.516 distance: 81 - 84: 15.021 distance: 82 - 83: 15.053 distance: 82 - 89: 7.530 distance: 84 - 85: 10.259 distance: 85 - 86: 7.345 distance: 86 - 87: 8.627 distance: 86 - 88: 6.283