Starting phenix.real_space_refine on Thu Jun 5 06:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2z_44118/06_2025/9b2z_44118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2z_44118/06_2025/9b2z_44118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2z_44118/06_2025/9b2z_44118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2z_44118/06_2025/9b2z_44118.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2z_44118/06_2025/9b2z_44118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2z_44118/06_2025/9b2z_44118.cif" } resolution = 2.83 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= 0.036 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 Ca 1 9.91 5 P 4 5.49 5 S 26 5.16 5 C 3509 2.51 5 N 926 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2638 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 15, 'TRANS': 335} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2787 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' CA': 1, 'ATP': 1, 'LAB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.93, per 1000 atoms: 0.71 Number of scatterers: 5506 At special positions: 0 Unit cell: (71.514, 81.378, 112.614, 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) Ca 1 19.99 S 26 16.00 P 4 15.00 O 1040 8.00 N 926 7.00 C 3509 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 793.8 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 59.9% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.532A pdb=" N ALA A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 135 removed outlier: 3.688A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.507A pdb=" N ASN A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.500A pdb=" N GLN A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.549A pdb=" N LEU A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 301 Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.290A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 4.509A pdb=" N ILE A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.591A pdb=" N LYS A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.630A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.560A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.745A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.579A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.099A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 211 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.502A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.188A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 287 hydrogen bonds defined for protein. 780 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: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 897 1.30 - 1.43: 1414 1.43 - 1.56: 3261 1.56 - 1.69: 8 1.69 - 1.82: 45 Bond restraints: 5625 Sorted by residual: bond pdb=" C5 AMP A 601 " pdb=" N7 AMP A 601 " ideal model delta sigma weight residual 1.350 1.552 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" CE1 HIS A 305 " pdb=" NE2 HIS A 305 " ideal model delta sigma weight residual 1.321 1.408 -0.087 1.00e-02 1.00e+04 7.62e+01 bond pdb=" C4 ATP B 402 " pdb=" C5 ATP B 402 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" O1P AMP A 601 " pdb=" P AMP A 601 " ideal model delta sigma weight residual 1.510 1.654 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C5 ATP B 402 " pdb=" C6 ATP B 402 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.07e+01 ... (remaining 5620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 7571 3.25 - 6.50: 64 6.50 - 9.75: 11 9.75 - 13.01: 1 13.01 - 16.26: 3 Bond angle restraints: 7650 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 123.61 16.26 1.00e+00 1.00e+00 2.64e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 122.51 14.32 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N3 ATP B 402 " ideal model delta sigma weight residual 126.80 118.89 7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" CA HIS A 305 " pdb=" CB HIS A 305 " pdb=" CG HIS A 305 " ideal model delta sigma weight residual 113.80 106.90 6.90 1.00e+00 1.00e+00 4.76e+01 angle pdb=" N3 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N9 ATP B 402 " ideal model delta sigma weight residual 127.04 134.80 -7.76 1.15e+00 7.59e-01 4.56e+01 ... (remaining 7645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 3342 31.47 - 62.95: 80 62.95 - 94.42: 9 94.42 - 125.89: 5 125.89 - 157.36: 2 Dihedral angle restraints: 3438 sinusoidal: 1348 harmonic: 2090 Sorted by residual: dihedral pdb=" C2 LAB B 401 " pdb=" C3 LAB B 401 " pdb=" C4 LAB B 401 " pdb=" C5 LAB B 401 " ideal model delta sinusoidal sigma weight residual 275.91 118.55 157.36 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C11 LAB B 401 " pdb=" C10 LAB B 401 " pdb=" C9 LAB B 401 " pdb=" C8 LAB B 401 " ideal model delta sinusoidal sigma weight residual 129.60 -77.75 -152.65 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C3 LAB B 401 " pdb=" C1 LAB B 401 " pdb=" C2 LAB B 401 " pdb=" O2 LAB B 401 " ideal model delta sinusoidal sigma weight residual -142.77 -20.23 -122.54 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 3435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 866 0.118 - 0.236: 12 0.236 - 0.353: 2 0.353 - 0.471: 0 0.471 - 0.589: 1 Chirality restraints: 881 Sorted by residual: chirality pdb=" C16 LAB B 401 " pdb=" C15 LAB B 401 " pdb=" C17 LAB B 401 " pdb=" N1 LAB B 401 " both_signs ideal model delta sigma weight residual False 2.52 3.11 -0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" C15 LAB B 401 " pdb=" C14 LAB B 401 " pdb=" C16 LAB B 401 " pdb=" O3 LAB B 401 " both_signs ideal model delta sigma weight residual False 2.52 2.82 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C13 LAB B 401 " pdb=" C12 LAB B 401 " pdb=" C14 LAB B 401 " pdb=" O2 LAB B 401 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 878 not shown) Planarity restraints: 967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 LAB B 401 " 0.097 2.00e-02 2.50e+03 2.31e-01 5.36e+02 pdb=" C6 LAB B 401 " -0.308 2.00e-02 2.50e+03 pdb=" C7 LAB B 401 " 0.315 2.00e-02 2.50e+03 pdb=" C8 LAB B 401 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 LAB B 401 " -0.242 2.00e-02 2.50e+03 2.03e-01 5.14e+02 pdb=" C19 LAB B 401 " -0.158 2.00e-02 2.50e+03 pdb=" C2 LAB B 401 " 0.344 2.00e-02 2.50e+03 pdb=" C3 LAB B 401 " 0.062 2.00e-02 2.50e+03 pdb=" C4 LAB B 401 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 229 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 230 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.022 5.00e-02 4.00e+02 ... (remaining 964 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 452 2.74 - 3.28: 5621 3.28 - 3.82: 9343 3.82 - 4.36: 11808 4.36 - 4.90: 19779 Nonbonded interactions: 47003 Sorted by model distance: nonbonded pdb=" O PHE A 174 " pdb=" OG SER A 177 " model vdw 2.200 3.040 nonbonded pdb=" O ALA B 174 " pdb=" OG SER B 281 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR B 160 " pdb=" O LEU B 180 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP B 157 " pdb=" O3' ATP B 402 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 307 " pdb=" O TYR A 332 " model vdw 2.253 3.040 ... (remaining 46998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.330 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.007 0.202 5626 Z= 0.426 Angle : 0.812 16.257 7650 Z= 0.502 Chirality : 0.050 0.589 881 Planarity : 0.011 0.231 967 Dihedral : 15.826 157.363 2086 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.18 % Allowed : 0.88 % Favored : 98.94 % 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: -0.65 (0.31), residues: 705 helix: -0.11 (0.27), residues: 362 sheet: -0.99 (0.71), residues: 55 loop : -0.53 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.013 0.002 PHE A 86 TYR 0.023 0.001 TYR A 299 ARG 0.007 0.001 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.14541 ( 287) hydrogen bonds : angle 6.24492 ( 780) covalent geometry : bond 0.00703 ( 5625) covalent geometry : angle 0.81194 ( 7650) Misc. bond : bond 0.05451 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.616 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 1.3550 time to fit residues: 115.6302 Evaluate side-chains 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.165545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138620 restraints weight = 5613.501| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.59 r_work: 0.3745 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5626 Z= 0.136 Angle : 0.574 7.595 7650 Z= 0.285 Chirality : 0.042 0.142 881 Planarity : 0.004 0.035 967 Dihedral : 12.854 159.952 849 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.88 % Allowed : 8.14 % Favored : 90.97 % 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: -0.15 (0.32), residues: 705 helix: 0.30 (0.27), residues: 367 sheet: -0.83 (0.71), residues: 55 loop : -0.29 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.010 0.001 PHE B 31 TYR 0.018 0.001 TYR A 299 ARG 0.005 0.001 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 287) hydrogen bonds : angle 4.80437 ( 780) covalent geometry : bond 0.00319 ( 5625) covalent geometry : angle 0.57354 ( 7650) Misc. bond : bond 0.00179 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.669 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.8943 time to fit residues: 71.2922 Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 363 GLN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.162943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135668 restraints weight = 5718.412| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.61 r_work: 0.3740 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5626 Z= 0.194 Angle : 0.621 7.914 7650 Z= 0.309 Chirality : 0.045 0.165 881 Planarity : 0.004 0.035 967 Dihedral : 12.430 161.032 849 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.42 % Allowed : 10.80 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.32), residues: 705 helix: 0.15 (0.27), residues: 366 sheet: -0.80 (0.72), residues: 54 loop : -0.31 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 295 HIS 0.004 0.001 HIS A 305 PHE 0.014 0.002 PHE A 86 TYR 0.020 0.001 TYR A 299 ARG 0.004 0.001 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 287) hydrogen bonds : angle 4.83016 ( 780) covalent geometry : bond 0.00472 ( 5625) covalent geometry : angle 0.62080 ( 7650) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.639 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.9036 time to fit residues: 66.3946 Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.165377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.137888 restraints weight = 5848.242| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.64 r_work: 0.3793 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5626 Z= 0.138 Angle : 0.559 7.668 7650 Z= 0.276 Chirality : 0.042 0.139 881 Planarity : 0.004 0.034 967 Dihedral : 12.223 163.236 849 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.77 % Allowed : 12.04 % Favored : 86.19 % 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: -0.02 (0.32), residues: 705 helix: 0.29 (0.27), residues: 378 sheet: -0.68 (0.72), residues: 54 loop : -0.07 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.009 0.001 PHE A 86 TYR 0.013 0.001 TYR A 299 ARG 0.002 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 287) hydrogen bonds : angle 4.53059 ( 780) covalent geometry : bond 0.00326 ( 5625) covalent geometry : angle 0.55947 ( 7650) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.646 Fit side-chains REVERT: B 72 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: B 207 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: B 248 ILE cc_start: 0.7831 (pt) cc_final: 0.7477 (pt) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.9201 time to fit residues: 72.4110 Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.166952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139678 restraints weight = 5714.778| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.62 r_work: 0.3765 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5626 Z= 0.120 Angle : 0.539 7.770 7650 Z= 0.264 Chirality : 0.041 0.140 881 Planarity : 0.004 0.033 967 Dihedral : 12.112 165.050 849 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.48 % Allowed : 13.45 % Favored : 84.07 % 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 (0.32), residues: 705 helix: 0.49 (0.27), residues: 379 sheet: -0.93 (0.68), residues: 60 loop : 0.10 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.008 0.001 PHE A 366 TYR 0.010 0.001 TYR A 299 ARG 0.002 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 287) hydrogen bonds : angle 4.37377 ( 780) covalent geometry : bond 0.00282 ( 5625) covalent geometry : angle 0.53896 ( 7650) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.604 Fit side-chains REVERT: A 74 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6677 (mp-120) REVERT: B 28 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7807 (mtm110) REVERT: B 72 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: B 207 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6789 (mm-30) REVERT: B 248 ILE cc_start: 0.7873 (pt) cc_final: 0.7482 (pt) outliers start: 14 outliers final: 4 residues processed: 80 average time/residue: 0.8835 time to fit residues: 75.0359 Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 54.1702 > 50: distance: 0 - 1: 39.976 distance: 1 - 2: 25.803 distance: 1 - 4: 4.843 distance: 2 - 3: 14.093 distance: 2 - 8: 40.788 distance: 4 - 5: 38.551 distance: 4 - 6: 12.894 distance: 5 - 7: 8.234 distance: 10 - 13: 16.932 distance: 13 - 14: 9.951 distance: 14 - 15: 16.305 distance: 14 - 17: 19.719 distance: 15 - 16: 14.076 distance: 15 - 18: 10.442 distance: 18 - 19: 17.543 distance: 19 - 20: 10.854 distance: 19 - 22: 6.872 distance: 20 - 21: 12.743 distance: 20 - 26: 12.100 distance: 22 - 23: 10.371 distance: 23 - 24: 11.717 distance: 23 - 25: 19.195 distance: 26 - 27: 9.580 distance: 26 - 97: 7.444 distance: 27 - 28: 18.938 distance: 27 - 30: 13.585 distance: 28 - 29: 17.910 distance: 28 - 33: 22.808 distance: 29 - 94: 33.622 distance: 30 - 31: 7.205 distance: 30 - 32: 33.554 distance: 33 - 34: 15.007 distance: 34 - 35: 28.441 distance: 34 - 37: 13.039 distance: 35 - 36: 27.053 distance: 35 - 40: 27.921 distance: 37 - 38: 14.554 distance: 37 - 39: 19.919 distance: 40 - 41: 15.587 distance: 40 - 83: 10.558 distance: 41 - 42: 32.545 distance: 41 - 44: 11.594 distance: 42 - 43: 6.195 distance: 42 - 48: 23.960 distance: 43 - 80: 33.605 distance: 44 - 45: 32.413 distance: 45 - 46: 19.888 distance: 45 - 47: 17.223 distance: 48 - 49: 7.327 distance: 49 - 50: 16.835 distance: 49 - 52: 10.679 distance: 50 - 51: 14.607 distance: 50 - 56: 28.523 distance: 52 - 53: 11.134 distance: 53 - 54: 10.821 distance: 53 - 55: 12.497 distance: 56 - 57: 14.459 distance: 57 - 58: 9.485 distance: 58 - 59: 9.661 distance: 58 - 60: 9.625