Starting phenix.real_space_refine on Fri Aug 22 14:13:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1k_44082/08_2025/9b1k_44082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1k_44082/08_2025/9b1k_44082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b1k_44082/08_2025/9b1k_44082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1k_44082/08_2025/9b1k_44082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b1k_44082/08_2025/9b1k_44082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1k_44082/08_2025/9b1k_44082.map" } resolution = 3.3 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= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2548 2.51 5 N 661 2.21 5 O 672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3911 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3899 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 29, 'TRANS': 482} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.35 Number of scatterers: 3911 At special positions: 0 Unit cell: (57.761, 102.542, 89.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 672 8.00 N 661 7.00 C 2548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 185.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 944 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 82.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.512A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.515A pdb=" N ALA A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.786A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.965A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.622A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.717A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 222 No H-bonds generated for 'chain 'A' and resid 221 through 222' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.297A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.828A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 4.080A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 removed outlier: 4.163A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.911A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.536A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.518A pdb=" N VAL A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 364 removed outlier: 3.561A pdb=" N PHE A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.572A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.613A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 426 through 455 Processing helix chain 'A' and resid 460 through 485 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.933A pdb=" N VAL A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.758A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 269 hydrogen bonds defined for protein. 777 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: 0.67 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1232 1.34 - 1.46: 955 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4011 Sorted by residual: bond pdb=" C2 URC A 901 " pdb=" O11 URC A 901 " ideal model delta sigma weight residual 1.213 1.360 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 1.215 1.350 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C4 URC A 901 " pdb=" C5 URC A 901 " ideal model delta sigma weight residual 1.358 1.488 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C6 URC A 901 " pdb=" O13 URC A 901 " ideal model delta sigma weight residual 1.218 1.345 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C4 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 4006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 5417 2.68 - 5.35: 44 5.35 - 8.03: 5 8.03 - 10.70: 4 10.70 - 13.38: 3 Bond angle restraints: 5473 Sorted by residual: angle pdb=" N1 URC A 901 " pdb=" C2 URC A 901 " pdb=" N3 URC A 901 " ideal model delta sigma weight residual 114.62 128.00 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C2 URC A 901 " pdb=" N1 URC A 901 " pdb=" C6 URC A 901 " ideal model delta sigma weight residual 129.31 117.61 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 104.73 116.27 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C5 URC A 901 " pdb=" C6 URC A 901 " pdb=" N1 URC A 901 " ideal model delta sigma weight residual 111.19 121.73 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 129.09 119.74 9.35 3.00e+00 1.11e-01 9.72e+00 ... (remaining 5468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2189 15.54 - 31.08: 143 31.08 - 46.62: 16 46.62 - 62.16: 5 62.16 - 77.70: 2 Dihedral angle restraints: 2355 sinusoidal: 892 harmonic: 1463 Sorted by residual: dihedral pdb=" CA GLU A 329 " pdb=" C GLU A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS A 286 " pdb=" C LYS A 286 " pdb=" N GLY A 287 " pdb=" CA GLY A 287 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB MET A 36 " pdb=" CG MET A 36 " pdb=" SD MET A 36 " pdb=" CE MET A 36 " ideal model delta sinusoidal sigma weight residual 180.00 129.26 50.74 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 2352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 380 0.026 - 0.053: 177 0.053 - 0.079: 52 0.079 - 0.105: 25 0.105 - 0.131: 8 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL A 422 " pdb=" N VAL A 422 " pdb=" C VAL A 422 " pdb=" CB VAL A 422 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL A 118 " pdb=" N VAL A 118 " pdb=" C VAL A 118 " pdb=" CB VAL A 118 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 639 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 276 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 277 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 264 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 265 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO A 480 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.015 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 968 2.79 - 3.32: 3936 3.32 - 3.85: 6497 3.85 - 4.37: 7738 4.37 - 4.90: 12839 Nonbonded interactions: 31978 Sorted by model distance: nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.265 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.346 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.410 3.040 nonbonded pdb=" O PHE A 270 " pdb=" OG SER A 273 " model vdw 2.411 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.424 3.040 ... (remaining 31973 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.670 Find NCS groups from input model: 0.020 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.006 0.147 4013 Z= 0.298 Angle : 0.741 13.375 5477 Z= 0.355 Chirality : 0.037 0.131 642 Planarity : 0.004 0.034 680 Dihedral : 10.547 77.700 1405 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: 0.11 (0.37), residues: 510 helix: 0.05 (0.26), residues: 375 sheet: -1.86 (1.54), residues: 10 loop : 0.91 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 15 TYR 0.011 0.001 TYR A 272 PHE 0.014 0.001 PHE A 270 TRP 0.009 0.001 TRP A 491 HIS 0.002 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 4011) covalent geometry : angle 0.73883 ( 5473) SS BOND : bond 0.00042 ( 2) SS BOND : angle 2.07348 ( 4) hydrogen bonds : bond 0.13338 ( 269) hydrogen bonds : angle 5.87484 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.135 Fit side-chains REVERT: A 22 MET cc_start: 0.7160 (ttm) cc_final: 0.6490 (ttp) REVERT: A 56 ASN cc_start: 0.7463 (t0) cc_final: 0.7147 (t0) REVERT: A 166 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7178 (tpp80) REVERT: A 231 MET cc_start: 0.7036 (mmm) cc_final: 0.6787 (mmt) REVERT: A 234 ASN cc_start: 0.8722 (t0) cc_final: 0.8462 (t0) REVERT: A 291 GLN cc_start: 0.7796 (mt0) cc_final: 0.7227 (tt0) REVERT: A 367 LEU cc_start: 0.8448 (mt) cc_final: 0.8182 (mp) REVERT: A 374 ILE cc_start: 0.7877 (pt) cc_final: 0.7643 (tt) REVERT: A 491 TRP cc_start: 0.4952 (t60) cc_final: 0.4749 (t60) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0675 time to fit residues: 6.9821 Evaluate side-chains 59 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.0010 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.194818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152103 restraints weight = 4625.835| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.32 r_work: 0.3407 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4013 Z= 0.141 Angle : 0.568 5.715 5477 Z= 0.292 Chirality : 0.039 0.134 642 Planarity : 0.005 0.046 680 Dihedral : 4.389 16.216 545 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.45 % Allowed : 6.54 % Favored : 92.01 % 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: 1.02 (0.38), residues: 510 helix: 0.77 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.82 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 473 TYR 0.016 0.001 TYR A 272 PHE 0.010 0.001 PHE A 270 TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4011) covalent geometry : angle 0.56534 ( 5473) SS BOND : bond 0.00089 ( 2) SS BOND : angle 2.01771 ( 4) hydrogen bonds : bond 0.05094 ( 269) hydrogen bonds : angle 4.66142 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.143 Fit side-chains REVERT: A 22 MET cc_start: 0.6825 (ttm) cc_final: 0.6410 (ptt) REVERT: A 56 ASN cc_start: 0.7205 (t0) cc_final: 0.6786 (t0) REVERT: A 166 ARG cc_start: 0.7630 (ttt180) cc_final: 0.7034 (tpp80) REVERT: A 231 MET cc_start: 0.6961 (mmm) cc_final: 0.6719 (mmt) REVERT: A 234 ASN cc_start: 0.8711 (t0) cc_final: 0.8510 (t0) REVERT: A 462 MET cc_start: 0.6346 (tpt) cc_final: 0.5827 (tpt) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.0631 time to fit residues: 5.4818 Evaluate side-chains 58 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 399 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.187403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143372 restraints weight = 4632.247| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.34 r_work: 0.3381 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4013 Z= 0.148 Angle : 0.568 5.928 5477 Z= 0.285 Chirality : 0.039 0.165 642 Planarity : 0.005 0.039 680 Dihedral : 4.230 15.620 545 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.69 % Allowed : 8.72 % Favored : 89.59 % 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: 0.97 (0.38), residues: 510 helix: 0.84 (0.27), residues: 383 sheet: -2.26 (1.70), residues: 10 loop : 0.68 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 15 TYR 0.018 0.001 TYR A 272 PHE 0.010 0.001 PHE A 358 TRP 0.013 0.001 TRP A 491 HIS 0.002 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4011) covalent geometry : angle 0.56559 ( 5473) SS BOND : bond 0.00098 ( 2) SS BOND : angle 2.01625 ( 4) hydrogen bonds : bond 0.04902 ( 269) hydrogen bonds : angle 4.50289 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.146 Fit side-chains REVERT: A 5 GLU cc_start: 0.6821 (pm20) cc_final: 0.6475 (pm20) REVERT: A 22 MET cc_start: 0.6826 (ttm) cc_final: 0.6406 (ptt) REVERT: A 56 ASN cc_start: 0.7192 (t0) cc_final: 0.6739 (t0) REVERT: A 166 ARG cc_start: 0.7647 (ttt180) cc_final: 0.7026 (tpp80) REVERT: A 491 TRP cc_start: 0.4806 (t60) cc_final: 0.4435 (p-90) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.0503 time to fit residues: 4.4073 Evaluate side-chains 61 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 374 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.188110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143869 restraints weight = 4621.398| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.33 r_work: 0.3418 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4013 Z= 0.113 Angle : 0.503 5.618 5477 Z= 0.252 Chirality : 0.037 0.143 642 Planarity : 0.005 0.041 680 Dihedral : 3.946 14.293 545 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.94 % Allowed : 8.96 % Favored : 89.10 % 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: 1.31 (0.37), residues: 510 helix: 1.17 (0.27), residues: 376 sheet: -2.22 (1.76), residues: 10 loop : 0.50 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 15 TYR 0.017 0.001 TYR A 272 PHE 0.009 0.001 PHE A 201 TRP 0.011 0.001 TRP A 491 HIS 0.002 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4011) covalent geometry : angle 0.50101 ( 5473) SS BOND : bond 0.00119 ( 2) SS BOND : angle 1.55356 ( 4) hydrogen bonds : bond 0.04235 ( 269) hydrogen bonds : angle 4.21379 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.138 Fit side-chains REVERT: A 22 MET cc_start: 0.6748 (ttm) cc_final: 0.6425 (ptt) REVERT: A 56 ASN cc_start: 0.7172 (t0) cc_final: 0.6693 (t0) REVERT: A 166 ARG cc_start: 0.7645 (ttt180) cc_final: 0.7021 (tpp80) REVERT: A 234 ASN cc_start: 0.8580 (t0) cc_final: 0.8250 (t0) REVERT: A 491 TRP cc_start: 0.4898 (t60) cc_final: 0.4669 (p-90) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.0518 time to fit residues: 5.0397 Evaluate side-chains 64 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 374 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 42 optimal weight: 0.0050 overall best weight: 0.3532 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.188621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143759 restraints weight = 4694.983| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.39 r_work: 0.3446 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4013 Z= 0.112 Angle : 0.515 6.588 5477 Z= 0.253 Chirality : 0.037 0.126 642 Planarity : 0.004 0.041 680 Dihedral : 3.800 13.331 545 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.18 % Allowed : 10.41 % Favored : 87.41 % 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: 1.70 (0.37), residues: 510 helix: 1.45 (0.27), residues: 373 sheet: -1.88 (1.90), residues: 10 loop : 0.70 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 483 TYR 0.015 0.001 TYR A 272 PHE 0.012 0.001 PHE A 201 TRP 0.009 0.001 TRP A 491 HIS 0.001 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4011) covalent geometry : angle 0.51365 ( 5473) SS BOND : bond 0.00114 ( 2) SS BOND : angle 1.44788 ( 4) hydrogen bonds : bond 0.04152 ( 269) hydrogen bonds : angle 4.14820 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.161 Fit side-chains REVERT: A 22 MET cc_start: 0.6644 (ttm) cc_final: 0.6327 (ptt) REVERT: A 56 ASN cc_start: 0.7171 (t0) cc_final: 0.6665 (t0) REVERT: A 166 ARG cc_start: 0.7614 (ttt180) cc_final: 0.6944 (tpp80) outliers start: 9 outliers final: 9 residues processed: 68 average time/residue: 0.0466 time to fit residues: 4.3114 Evaluate side-chains 69 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.190048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147244 restraints weight = 4633.699| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.33 r_work: 0.3426 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4013 Z= 0.144 Angle : 0.544 6.585 5477 Z= 0.270 Chirality : 0.039 0.127 642 Planarity : 0.005 0.042 680 Dihedral : 3.911 13.522 545 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.91 % Allowed : 10.17 % Favored : 86.92 % 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: 1.54 (0.38), residues: 510 helix: 1.27 (0.27), residues: 381 sheet: -2.30 (1.85), residues: 10 loop : 0.85 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.019 0.002 TYR A 272 PHE 0.011 0.001 PHE A 358 TRP 0.009 0.001 TRP A 50 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4011) covalent geometry : angle 0.54234 ( 5473) SS BOND : bond 0.00185 ( 2) SS BOND : angle 1.75068 ( 4) hydrogen bonds : bond 0.04640 ( 269) hydrogen bonds : angle 4.26736 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.091 Fit side-chains REVERT: A 22 MET cc_start: 0.6886 (ttm) cc_final: 0.6465 (ptt) REVERT: A 56 ASN cc_start: 0.7212 (t0) cc_final: 0.6725 (t0) REVERT: A 166 ARG cc_start: 0.7666 (ttt180) cc_final: 0.6962 (tpp80) REVERT: A 234 ASN cc_start: 0.8655 (t0) cc_final: 0.8448 (t0) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 0.0478 time to fit residues: 4.3915 Evaluate side-chains 69 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.183851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139014 restraints weight = 4734.909| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.44 r_work: 0.3382 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4013 Z= 0.124 Angle : 0.512 6.705 5477 Z= 0.255 Chirality : 0.038 0.126 642 Planarity : 0.004 0.042 680 Dihedral : 3.829 13.479 545 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.15 % Allowed : 10.41 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.38), residues: 510 helix: 1.37 (0.27), residues: 379 sheet: -1.97 (1.97), residues: 10 loop : 0.82 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.017 0.001 TYR A 272 PHE 0.009 0.001 PHE A 201 TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4011) covalent geometry : angle 0.51081 ( 5473) SS BOND : bond 0.00177 ( 2) SS BOND : angle 1.49997 ( 4) hydrogen bonds : bond 0.04361 ( 269) hydrogen bonds : angle 4.19674 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.123 Fit side-chains REVERT: A 5 GLU cc_start: 0.7139 (pm20) cc_final: 0.6895 (pm20) REVERT: A 22 MET cc_start: 0.6773 (ttm) cc_final: 0.6436 (ptt) REVERT: A 56 ASN cc_start: 0.7211 (t0) cc_final: 0.6711 (t0) REVERT: A 166 ARG cc_start: 0.7670 (ttt180) cc_final: 0.6973 (tpp80) REVERT: A 234 ASN cc_start: 0.8581 (t0) cc_final: 0.8380 (t0) REVERT: A 385 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7540 (m-30) outliers start: 13 outliers final: 12 residues processed: 69 average time/residue: 0.0447 time to fit residues: 4.2295 Evaluate side-chains 73 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144767 restraints weight = 4637.991| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.35 r_work: 0.3394 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4013 Z= 0.143 Angle : 0.566 10.535 5477 Z= 0.274 Chirality : 0.039 0.143 642 Planarity : 0.004 0.042 680 Dihedral : 3.887 14.221 545 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.39 % Allowed : 10.65 % Favored : 85.96 % 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: 1.55 (0.38), residues: 510 helix: 1.18 (0.26), residues: 387 sheet: -1.81 (2.11), residues: 10 loop : 1.22 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.020 0.001 TYR A 272 PHE 0.010 0.001 PHE A 266 TRP 0.010 0.001 TRP A 50 HIS 0.001 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4011) covalent geometry : angle 0.56407 ( 5473) SS BOND : bond 0.00206 ( 2) SS BOND : angle 1.62617 ( 4) hydrogen bonds : bond 0.04602 ( 269) hydrogen bonds : angle 4.31756 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.207 Fit side-chains REVERT: A 22 MET cc_start: 0.6801 (ttm) cc_final: 0.6420 (ptt) REVERT: A 56 ASN cc_start: 0.7244 (t0) cc_final: 0.6745 (t0) REVERT: A 166 ARG cc_start: 0.7653 (ttt180) cc_final: 0.6962 (tpp80) REVERT: A 385 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7576 (m-30) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.0554 time to fit residues: 5.0832 Evaluate side-chains 69 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.188271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145020 restraints weight = 4651.119| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.35 r_work: 0.3389 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4013 Z= 0.139 Angle : 0.556 8.131 5477 Z= 0.272 Chirality : 0.039 0.139 642 Planarity : 0.004 0.042 680 Dihedral : 3.856 13.723 545 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.15 % Allowed : 10.65 % Favored : 86.20 % 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: 1.68 (0.38), residues: 510 helix: 1.26 (0.27), residues: 384 sheet: -1.91 (2.05), residues: 10 loop : 1.33 (0.63), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.020 0.001 TYR A 272 PHE 0.009 0.001 PHE A 358 TRP 0.010 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4011) covalent geometry : angle 0.55510 ( 5473) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.53229 ( 4) hydrogen bonds : bond 0.04555 ( 269) hydrogen bonds : angle 4.27965 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.174 Fit side-chains REVERT: A 22 MET cc_start: 0.6871 (ttm) cc_final: 0.6502 (ptt) REVERT: A 56 ASN cc_start: 0.7271 (t0) cc_final: 0.6767 (t0) REVERT: A 88 PHE cc_start: 0.7982 (m-10) cc_final: 0.7675 (m-10) REVERT: A 166 ARG cc_start: 0.7699 (ttt180) cc_final: 0.6996 (tpp80) REVERT: A 385 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7597 (m-30) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.0487 time to fit residues: 4.2096 Evaluate side-chains 71 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 56.6042 > 50: distance: 2 - 23: 4.622 distance: 7 - 31: 5.190 distance: 12 - 36: 9.459 distance: 19 - 44: 8.389 distance: 23 - 24: 6.236 distance: 24 - 25: 8.300 distance: 24 - 27: 13.374 distance: 25 - 31: 3.031 distance: 26 - 52: 3.045 distance: 27 - 28: 11.340 distance: 28 - 29: 8.642 distance: 29 - 30: 7.597 distance: 32 - 33: 4.728 distance: 32 - 35: 6.339 distance: 34 - 59: 15.498 distance: 36 - 37: 3.897 distance: 37 - 40: 4.971 distance: 38 - 39: 5.223 distance: 39 - 65: 34.959 distance: 41 - 42: 3.250 distance: 41 - 43: 6.078 distance: 44 - 45: 8.480 distance: 45 - 46: 4.784 distance: 45 - 48: 5.320 distance: 46 - 47: 9.520 distance: 46 - 52: 6.972 distance: 47 - 73: 25.286 distance: 48 - 49: 7.758 distance: 49 - 50: 4.709 distance: 50 - 51: 5.767 distance: 52 - 53: 8.778 distance: 53 - 54: 8.739 distance: 53 - 56: 9.580 distance: 54 - 59: 4.815 distance: 55 - 81: 15.773 distance: 56 - 57: 11.481 distance: 56 - 58: 11.096 distance: 59 - 60: 5.465 distance: 60 - 61: 7.933 distance: 60 - 63: 9.918 distance: 61 - 62: 11.898 distance: 61 - 65: 34.645 distance: 62 - 95: 7.539 distance: 63 - 64: 15.053 distance: 65 - 66: 33.416 distance: 66 - 67: 5.208 distance: 66 - 69: 23.508 distance: 67 - 68: 16.905 distance: 67 - 73: 13.909 distance: 68 - 103: 22.827 distance: 69 - 70: 16.376 distance: 69 - 71: 12.324 distance: 70 - 72: 17.115 distance: 73 - 74: 6.680 distance: 74 - 75: 6.434 distance: 74 - 77: 4.471 distance: 75 - 76: 9.100 distance: 75 - 81: 3.596 distance: 76 - 109: 6.269 distance: 77 - 78: 4.858 distance: 78 - 79: 6.551 distance: 79 - 80: 7.113 distance: 82 - 83: 3.226 distance: 82 - 85: 3.460 distance: 83 - 95: 4.531 distance: 84 - 116: 6.728 distance: 86 - 87: 3.629 distance: 86 - 88: 3.353 distance: 88 - 90: 3.564 distance: 88 - 91: 4.470 distance: 89 - 90: 4.068 distance: 90 - 92: 4.116 distance: 91 - 93: 3.302 distance: 96 - 97: 5.277 distance: 96 - 99: 4.897 distance: 98 - 123: 7.888 distance: 99 - 100: 4.899 distance: 100 - 101: 21.826 distance: 100 - 102: 12.433