Starting phenix.real_space_refine on Fri Aug 22 13:16:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrr_18624/08_2025/8qrr_18624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrr_18624/08_2025/8qrr_18624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2025/8qrr_18624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2025/8qrr_18624.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2025/8qrr_18624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2025/8qrr_18624.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 16 5.16 5 Na 3 4.78 5 C 2052 2.51 5 N 512 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3129 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3116 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 16, 'TRANS': 403} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 0.94, per 1000 atoms: 0.30 Number of scatterers: 3129 At special positions: 0 Unit cell: (60.192, 70.224, 75.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 Na 3 11.00 O 546 8.00 N 512 7.00 C 2052 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: 0.22 Conformation dependent library (CDL) restraints added in 130.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 85.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 52 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 103 removed outlier: 3.687A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.795A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 249 through 292 removed outlier: 4.530A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.731A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 383 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 4.110A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.522A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.640A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 260 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: 0.35 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 988 1.34 - 1.46: 426 1.46 - 1.57: 1742 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3181 Sorted by residual: bond pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.19e-01 bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.51e-01 bond pdb=" CG LEU B 107 " pdb=" CD1 LEU B 107 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" CG1 ILE B 104 " pdb=" CD1 ILE B 104 " ideal model delta sigma weight residual 1.513 1.490 0.023 3.90e-02 6.57e+02 3.35e-01 bond pdb=" CA VAL B 472 " pdb=" C VAL B 472 " ideal model delta sigma weight residual 1.523 1.516 0.007 1.27e-02 6.20e+03 3.31e-01 ... (remaining 3176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 4214 1.12 - 2.23: 80 2.23 - 3.35: 23 3.35 - 4.47: 8 4.47 - 5.58: 7 Bond angle restraints: 4332 Sorted by residual: angle pdb=" CB ARG B 301 " pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 111.30 116.88 -5.58 2.30e+00 1.89e-01 5.89e+00 angle pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " pdb=" NE ARG B 301 " ideal model delta sigma weight residual 112.00 117.10 -5.10 2.20e+00 2.07e-01 5.37e+00 angle pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " pdb=" CG2 VAL B 459 " ideal model delta sigma weight residual 110.40 114.29 -3.89 1.70e+00 3.46e-01 5.25e+00 angle pdb=" N ILE B 103 " pdb=" CA ILE B 103 " pdb=" C ILE B 103 " ideal model delta sigma weight residual 109.34 113.04 -3.70 2.08e+00 2.31e-01 3.16e+00 angle pdb=" N VAL B 459 " pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 112.16 110.10 2.06 1.30e+00 5.92e-01 2.51e+00 ... (remaining 4327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1669 17.95 - 35.89: 166 35.89 - 53.83: 28 53.83 - 71.78: 1 71.78 - 89.72: 3 Dihedral angle restraints: 1867 sinusoidal: 681 harmonic: 1186 Sorted by residual: dihedral pdb=" CA ASP B 294 " pdb=" CB ASP B 294 " pdb=" CG ASP B 294 " pdb=" OD1 ASP B 294 " ideal model delta sinusoidal sigma weight residual -30.00 -86.47 56.47 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " pdb=" CD GLU B 251 " pdb=" OE1 GLU B 251 " ideal model delta sinusoidal sigma weight residual 0.00 85.67 -85.67 1 3.00e+01 1.11e-03 9.86e+00 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -130.28 -49.72 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 1864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 468 0.059 - 0.118: 73 0.118 - 0.177: 1 0.177 - 0.235: 0 0.235 - 0.294: 1 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 540 not shown) Planarity restraints: 536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 474 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLY B 474 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY B 474 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B 475 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 471 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASN B 471 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 471 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 472 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 469 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL B 469 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 469 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 470 " -0.009 2.00e-02 2.50e+03 ... (remaining 533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 617 2.77 - 3.30: 3207 3.30 - 3.83: 5511 3.83 - 4.37: 6085 4.37 - 4.90: 11075 Nonbonded interactions: 26495 Sorted by model distance: nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.234 2.470 nonbonded pdb=" O PHE B 135 " pdb="NA NA B 603 " model vdw 2.255 2.470 nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.278 2.470 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.288 2.470 nonbonded pdb=" OG1 THR B 138 " pdb="NA NA B 603 " model vdw 2.310 2.470 ... (remaining 26490 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: 0.790 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.270 Find NCS groups from input model: 0.010 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:5.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 0.029 3181 Z= 0.122 Angle : 0.491 5.583 4332 Z= 0.255 Chirality : 0.039 0.294 543 Planarity : 0.005 0.055 536 Dihedral : 14.324 89.721 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.21 % Allowed : 18.48 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.43), residues: 414 helix: 1.96 (0.29), residues: 340 sheet: -1.40 (1.27), residues: 20 loop : -0.25 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 301 TYR 0.009 0.001 TYR B 334 PHE 0.008 0.001 PHE B 237 TRP 0.009 0.001 TRP B 338 HIS 0.001 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3181) covalent geometry : angle 0.49072 ( 4332) hydrogen bonds : bond 0.12153 ( 260) hydrogen bonds : angle 5.95125 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.086 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.3506 time to fit residues: 16.3172 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 410 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.129395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094286 restraints weight = 3679.523| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.97 r_work: 0.2950 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.137 Angle : 0.510 6.134 4332 Z= 0.254 Chirality : 0.039 0.200 543 Planarity : 0.004 0.030 536 Dihedral : 3.798 30.958 446 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.33 % Allowed : 16.97 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.43), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: -1.37 (1.28), residues: 20 loop : 0.01 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 301 TYR 0.010 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3181) covalent geometry : angle 0.50982 ( 4332) hydrogen bonds : bond 0.04370 ( 260) hydrogen bonds : angle 4.52619 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.098 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 51 average time/residue: 0.3214 time to fit residues: 17.0950 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2488 > 50: distance: 9 - 25: 3.570 distance: 17 - 36: 6.059 distance: 21 - 47: 12.812 distance: 26 - 27: 5.237 distance: 26 - 29: 8.278 distance: 27 - 31: 8.008 distance: 28 - 54: 7.481 distance: 29 - 30: 9.381 distance: 31 - 32: 4.335 distance: 32 - 33: 5.168 distance: 32 - 35: 11.372 distance: 33 - 34: 13.575 distance: 33 - 36: 3.477 distance: 36 - 37: 4.543 distance: 37 - 38: 5.905 distance: 37 - 40: 7.776 distance: 38 - 39: 3.810 distance: 38 - 47: 4.072 distance: 41 - 42: 5.902 distance: 41 - 43: 4.755 distance: 42 - 44: 6.797 distance: 43 - 45: 6.805 distance: 44 - 46: 5.591 distance: 45 - 46: 7.893 distance: 48 - 51: 5.082 distance: 51 - 52: 14.723 distance: 51 - 53: 11.070 distance: 55 - 56: 6.276 distance: 55 - 58: 7.376 distance: 56 - 57: 12.374 distance: 56 - 65: 10.411 distance: 57 - 85: 22.861 distance: 59 - 60: 11.091 distance: 60 - 62: 4.760 distance: 61 - 63: 5.018 distance: 62 - 64: 4.252 distance: 63 - 64: 6.503 distance: 65 - 66: 3.570 distance: 65 - 71: 10.134 distance: 66 - 67: 6.705 distance: 66 - 69: 10.399 distance: 67 - 68: 9.637 distance: 67 - 72: 12.594 distance: 68 - 93: 19.939 distance: 69 - 70: 11.231 distance: 70 - 71: 10.522 distance: 72 - 73: 8.872 distance: 73 - 74: 10.922 distance: 74 - 75: 7.426 distance: 74 - 76: 3.782 distance: 75 - 101: 22.581 distance: 76 - 77: 4.692 distance: 77 - 78: 12.729 distance: 77 - 80: 7.938 distance: 78 - 79: 23.707 distance: 78 - 85: 36.634 distance: 79 - 108: 23.794 distance: 80 - 81: 8.407 distance: 81 - 82: 8.579 distance: 82 - 83: 5.373 distance: 82 - 84: 7.572 distance: 85 - 86: 26.665 distance: 86 - 87: 10.281 distance: 86 - 89: 28.255 distance: 87 - 88: 5.814 distance: 87 - 93: 8.983 distance: 88 - 116: 12.413 distance: 89 - 90: 10.137 distance: 90 - 91: 14.459 distance: 90 - 92: 10.871 distance: 93 - 94: 5.500 distance: 94 - 95: 8.638 distance: 94 - 97: 10.018 distance: 95 - 101: 5.289 distance: 96 - 124: 6.262 distance: 97 - 98: 5.943 distance: 98 - 99: 5.302 distance: 98 - 100: 12.042 distance: 132 - 142: 3.569 distance: 145 - 152: 3.434 distance: 151 - 163: 3.046