Starting phenix.real_space_refine on Thu Mar 6 08:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugv_26497/03_2025/7ugv_26497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugv_26497/03_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_26497/03_2025/7ugv_26497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugv_26497/03_2025/7ugv_26497.map" model { file = "/net/cci-nas-00/data/ceres_data/7ugv_26497/03_2025/7ugv_26497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugv_26497/03_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-5624/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: 3.29, per 1000 atoms: 1.06 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: 0.80 Conformation dependent library (CDL) restraints added in 419.2 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: 0.33 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: 0.87 Time building geometry restraints manager: 0.94 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.720 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: 0.010 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- 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 : 0.349 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: 1.3900 time to fit residues: 81.3272 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 : 0.313 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.093871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.067182 restraints weight = 6011.250| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.60 r_work: 0.2744 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 44.912 445 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 : 0.316 Fit side-chains REVERT: A 5 ARG cc_start: 0.7448 (mmt90) cc_final: 0.6580 (mmt-90) REVERT: A 9 GLU cc_start: 0.8553 (mp0) cc_final: 0.7825 (mp0) REVERT: A 125 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8706 (t-90) REVERT: A 291 GLU cc_start: 0.8662 (mp0) cc_final: 0.8382 (mp0) REVERT: A 296 GLU cc_start: 0.9070 (tp30) cc_final: 0.8731 (tp30) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 1.3139 time to fit residues: 58.0912 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 : 0.329 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1232 > 50: distance: 15 - 20: 3.710 distance: 20 - 21: 4.418 distance: 21 - 24: 5.415 distance: 22 - 28: 3.325 distance: 23 - 50: 10.075 distance: 24 - 25: 8.199 distance: 25 - 26: 6.795 distance: 25 - 27: 7.635 distance: 28 - 29: 5.820 distance: 28 - 34: 7.825 distance: 29 - 30: 4.378 distance: 29 - 32: 4.994 distance: 30 - 31: 9.133 distance: 30 - 35: 7.128 distance: 32 - 33: 11.001 distance: 33 - 34: 11.155 distance: 38 - 63: 21.198 distance: 39 - 40: 3.975 distance: 46 - 47: 4.608 distance: 47 - 48: 6.609 distance: 48 - 49: 5.479 distance: 48 - 50: 8.745 distance: 51 - 52: 6.288 distance: 51 - 54: 7.699 distance: 52 - 53: 6.989 distance: 52 - 55: 8.678 distance: 53 - 76: 8.243 distance: 55 - 56: 4.980 distance: 56 - 57: 5.855 distance: 56 - 59: 3.328 distance: 57 - 58: 24.110 distance: 57 - 63: 29.252 distance: 60 - 61: 16.813 distance: 60 - 62: 18.571 distance: 63 - 64: 25.238 distance: 64 - 65: 22.108 distance: 64 - 67: 7.637 distance: 65 - 66: 11.554 distance: 65 - 68: 29.891 distance: 68 - 69: 6.828 distance: 69 - 70: 11.033 distance: 69 - 72: 5.440 distance: 70 - 71: 8.718 distance: 70 - 76: 6.470 distance: 72 - 73: 8.879 distance: 73 - 74: 8.658 distance: 73 - 75: 8.191 distance: 77 - 78: 5.135 distance: 78 - 79: 4.852 distance: 78 - 80: 3.390 distance: 81 - 82: 3.948 distance: 84 - 85: 7.698 distance: 85 - 86: 5.553 distance: 86 - 87: 4.907 distance: 86 - 88: 4.800