Starting phenix.real_space_refine on Sat May 2 12:08:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iy7_60987/05_2026/9iy7_60987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iy7_60987/05_2026/9iy7_60987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iy7_60987/05_2026/9iy7_60987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iy7_60987/05_2026/9iy7_60987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iy7_60987/05_2026/9iy7_60987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iy7_60987/05_2026/9iy7_60987.map" } resolution = 3.27 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= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 26 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 3200 2.51 5 N 670 2.21 5 O 764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4664 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4314 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain: "A" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 350 Unusual residues: {' CL': 1, ' NA': 2, 'D10': 2, 'D12': 6, 'DD9': 5, 'JC9': 1, 'LMT': 1, 'NAG': 1, 'OCT': 5, 'Y01': 3} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.84, per 1000 atoms: 0.18 Number of scatterers: 4664 At special positions: 0 Unit cell: (85.455, 80.18, 73.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 26 16.00 Na 2 11.00 O 764 8.00 N 670 7.00 C 3200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " 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=3, symmetry=0 Links applied NAG-ASN " NAG A 707 " - " ASN A 208 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 92.6 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 75.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.688A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 4.033A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 128 through 144 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 3.910A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.799A pdb=" N ILE A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.982A pdb=" N VAL A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.720A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.045A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.842A pdb=" N ALA A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.505A pdb=" N ASP A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 419 through 454 removed outlier: 4.077A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 543 Processing helix chain 'A' and resid 545 through 559 removed outlier: 4.209A pdb=" N PHE A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 558 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 4.164A pdb=" N ILE A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 605 through 613 removed outlier: 3.648A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) 268 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: 0.37 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 711 1.33 - 1.45: 1359 1.45 - 1.57: 2684 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 4792 Sorted by residual: bond pdb=" C5 JC9 A 708 " pdb=" O1 JC9 A 708 " ideal model delta sigma weight residual 1.217 1.411 -0.194 2.00e-02 2.50e+03 9.44e+01 bond pdb=" C8 JC9 A 708 " pdb="CL1 JC9 A 708 " ideal model delta sigma weight residual 1.735 1.788 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C3' LMT A 706 " pdb=" O3' LMT A 706 " ideal model delta sigma weight residual 1.404 1.361 0.043 2.00e-02 2.50e+03 4.62e+00 bond pdb=" C6' LMT A 706 " pdb=" O6' LMT A 706 " ideal model delta sigma weight residual 1.407 1.364 0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C2B LMT A 706 " pdb=" O2B LMT A 706 " ideal model delta sigma weight residual 1.410 1.368 0.042 2.00e-02 2.50e+03 4.38e+00 ... (remaining 4787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 6365 2.62 - 5.23: 93 5.23 - 7.85: 15 7.85 - 10.46: 3 10.46 - 13.08: 3 Bond angle restraints: 6479 Sorted by residual: angle pdb=" C6 JC9 A 708 " pdb=" C5 JC9 A 708 " pdb=" O1 JC9 A 708 " ideal model delta sigma weight residual 121.29 108.21 13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C1 JC9 A 708 " pdb=" C5 JC9 A 708 " pdb=" O1 JC9 A 708 " ideal model delta sigma weight residual 121.39 108.36 13.03 3.00e+00 1.11e-01 1.89e+01 angle pdb=" C2 LMT A 706 " pdb=" C3 LMT A 706 " pdb=" C4 LMT A 706 " ideal model delta sigma weight residual 117.09 106.99 10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA CYS A 200 " pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " ideal model delta sigma weight residual 114.40 121.36 -6.96 2.30e+00 1.89e-01 9.16e+00 angle pdb=" C SER A 199 " pdb=" N CYS A 200 " pdb=" CA CYS A 200 " ideal model delta sigma weight residual 123.34 117.90 5.44 1.80e+00 3.09e-01 9.13e+00 ... (remaining 6474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 2596 22.12 - 44.24: 284 44.24 - 66.36: 51 66.36 - 88.48: 12 88.48 - 110.59: 15 Dihedral angle restraints: 2958 sinusoidal: 1391 harmonic: 1567 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual -86.00 -146.75 60.75 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" C4B LMT A 706 " pdb=" C2B LMT A 706 " pdb=" C3B LMT A 706 " pdb=" O2B LMT A 706 " ideal model delta sinusoidal sigma weight residual 174.48 63.89 110.59 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C1' LMT A 706 " pdb=" C2' LMT A 706 " pdb=" C3' LMT A 706 " pdb=" O3' LMT A 706 " ideal model delta sinusoidal sigma weight residual -176.68 -66.30 -110.38 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 531 0.049 - 0.097: 154 0.097 - 0.146: 29 0.146 - 0.195: 3 0.195 - 0.243: 4 Chirality restraints: 721 Sorted by residual: chirality pdb=" CBF Y01 A 722 " pdb=" CAS Y01 A 722 " pdb=" CBD Y01 A 722 " pdb=" CBH Y01 A 722 " both_signs ideal model delta sigma weight residual False -2.45 -2.20 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A 609 " pdb=" CA ILE A 609 " pdb=" CG1 ILE A 609 " pdb=" CG2 ILE A 609 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 150 " pdb=" CA ILE A 150 " pdb=" CG1 ILE A 150 " pdb=" CG2 ILE A 150 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 718 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 JC9 A 708 " 0.117 2.00e-02 2.50e+03 2.03e-01 4.10e+02 pdb=" C5 JC9 A 708 " -0.351 2.00e-02 2.50e+03 pdb=" C6 JC9 A 708 " 0.116 2.00e-02 2.50e+03 pdb=" O1 JC9 A 708 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 600 " -0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 601 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 601 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 601 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 267 " -0.020 2.00e-02 2.50e+03 1.20e-02 2.89e+00 pdb=" CG TYR A 267 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 267 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 267 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 267 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 267 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 267 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 267 " -0.015 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 22 2.47 - 3.08: 3321 3.08 - 3.68: 6775 3.68 - 4.29: 10759 4.29 - 4.90: 18098 Nonbonded interactions: 38975 Sorted by model distance: nonbonded pdb=" OD2 ASP A 437 " pdb="NA NA A 703 " model vdw 1.860 2.470 nonbonded pdb=" OG1 THR A 284 " pdb=" OD1 ASP A 437 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR A 121 " pdb="CL CL A 701 " model vdw 2.231 3.190 nonbonded pdb=" O ARG A 596 " pdb=" OG1 THR A 600 " model vdw 2.262 3.040 nonbonded pdb=" O ILE A 587 " pdb=" OG1 THR A 591 " model vdw 2.264 3.040 ... (remaining 38970 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: 0.670 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.780 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:0.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.008 0.194 4797 Z= 0.341 Angle : 0.841 13.080 6484 Z= 0.402 Chirality : 0.049 0.243 721 Planarity : 0.010 0.203 747 Dihedral : 19.705 110.595 1957 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.22 % Allowed : 19.39 % Favored : 80.39 % 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 are not related in a simple way. whole: -1.45 (0.36), residues: 538 helix: -0.42 (0.26), residues: 366 sheet: None (None), residues: 0 loop : -1.96 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 152 TYR 0.021 0.002 TYR A 267 PHE 0.023 0.002 PHE A 548 TRP 0.013 0.002 TRP A 271 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00764 ( 4792) covalent geometry : angle 0.83778 ( 6479) SS BOND : bond 0.00033 ( 1) SS BOND : angle 3.18339 ( 2) hydrogen bonds : bond 0.16688 ( 268) hydrogen bonds : angle 6.88973 ( 780) Misc. bond : bond 0.00325 ( 3) link_NAG-ASN : bond 0.00529 ( 1) link_NAG-ASN : angle 2.44022 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.081 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.0245 time to fit residues: 1.8762 Evaluate side-chains 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.143009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.121506 restraints weight = 4949.537| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.48 r_work: 0.3199 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4797 Z= 0.160 Angle : 0.643 8.046 6484 Z= 0.317 Chirality : 0.044 0.186 721 Planarity : 0.005 0.063 747 Dihedral : 11.336 58.488 1029 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.74 % Allowed : 16.78 % Favored : 81.48 % 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 are not related in a simple way. whole: -0.44 (0.37), residues: 538 helix: 0.32 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -1.52 (0.56), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 607 TYR 0.015 0.001 TYR A 267 PHE 0.017 0.001 PHE A 548 TRP 0.008 0.001 TRP A 103 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4792) covalent geometry : angle 0.63766 ( 6479) SS BOND : bond 0.00148 ( 1) SS BOND : angle 2.35780 ( 2) hydrogen bonds : bond 0.05436 ( 268) hydrogen bonds : angle 4.81252 ( 780) Misc. bond : bond 0.00219 ( 3) link_NAG-ASN : bond 0.00329 ( 1) link_NAG-ASN : angle 3.39176 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.082 Fit side-chains REVERT: A 229 GLU cc_start: 0.6849 (tt0) cc_final: 0.6570 (tt0) REVERT: A 241 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7395 (mtp85) REVERT: A 310 LEU cc_start: 0.7517 (tp) cc_final: 0.7306 (tt) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.0390 time to fit residues: 2.6870 Evaluate side-chains 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 437 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 33 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 overall best weight: 0.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.126916 restraints weight = 4848.876| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.46 r_work: 0.3236 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4797 Z= 0.114 Angle : 0.536 5.392 6484 Z= 0.272 Chirality : 0.040 0.169 721 Planarity : 0.004 0.055 747 Dihedral : 8.908 55.290 1027 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.40 % Allowed : 15.90 % Favored : 81.70 % 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 are not related in a simple way. whole: 0.28 (0.38), residues: 538 helix: 0.93 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.43 (0.55), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 607 TYR 0.011 0.001 TYR A 267 PHE 0.016 0.001 PHE A 548 TRP 0.011 0.001 TRP A 458 HIS 0.001 0.000 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4792) covalent geometry : angle 0.53087 ( 6479) SS BOND : bond 0.00102 ( 1) SS BOND : angle 1.93819 ( 2) hydrogen bonds : bond 0.04622 ( 268) hydrogen bonds : angle 4.33301 ( 780) Misc. bond : bond 0.00134 ( 3) link_NAG-ASN : bond 0.00440 ( 1) link_NAG-ASN : angle 3.04681 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.081 Fit side-chains REVERT: A 377 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6941 (t80) outliers start: 11 outliers final: 4 residues processed: 51 average time/residue: 0.0293 time to fit residues: 2.1973 Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 585 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.141497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.119628 restraints weight = 4944.506| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.51 r_work: 0.3174 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4797 Z= 0.194 Angle : 0.614 5.547 6484 Z= 0.314 Chirality : 0.044 0.154 721 Planarity : 0.005 0.050 747 Dihedral : 9.192 57.132 1027 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.18 % Allowed : 17.21 % Favored : 80.61 % 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 are not related in a simple way. whole: -0.05 (0.37), residues: 538 helix: 0.70 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -1.61 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 241 TYR 0.029 0.002 TYR A 267 PHE 0.021 0.002 PHE A 548 TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 4792) covalent geometry : angle 0.60935 ( 6479) SS BOND : bond 0.00222 ( 1) SS BOND : angle 2.48352 ( 2) hydrogen bonds : bond 0.05397 ( 268) hydrogen bonds : angle 4.56554 ( 780) Misc. bond : bond 0.00264 ( 3) link_NAG-ASN : bond 0.00224 ( 1) link_NAG-ASN : angle 2.88309 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.081 Fit side-chains REVERT: A 229 GLU cc_start: 0.7003 (tt0) cc_final: 0.6738 (tt0) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.0294 time to fit residues: 2.1128 Evaluate side-chains 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 585 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.143334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.121727 restraints weight = 4937.664| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.47 r_work: 0.3203 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4797 Z= 0.154 Angle : 0.571 7.854 6484 Z= 0.292 Chirality : 0.042 0.193 721 Planarity : 0.004 0.042 747 Dihedral : 8.775 58.822 1027 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.05 % Allowed : 16.12 % Favored : 80.83 % 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 are not related in a simple way. whole: 0.06 (0.37), residues: 538 helix: 0.75 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -1.52 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 241 TYR 0.021 0.001 TYR A 267 PHE 0.019 0.001 PHE A 548 TRP 0.010 0.001 TRP A 458 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4792) covalent geometry : angle 0.56728 ( 6479) SS BOND : bond 0.00138 ( 1) SS BOND : angle 2.11347 ( 2) hydrogen bonds : bond 0.05005 ( 268) hydrogen bonds : angle 4.41906 ( 780) Misc. bond : bond 0.00219 ( 3) link_NAG-ASN : bond 0.00299 ( 1) link_NAG-ASN : angle 2.73025 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.080 Fit side-chains REVERT: A 229 GLU cc_start: 0.6820 (tt0) cc_final: 0.6572 (tt0) REVERT: A 430 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7342 (ttp) outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.0359 time to fit residues: 2.4312 Evaluate side-chains 47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 528 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.143875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.122109 restraints weight = 4956.853| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.49 r_work: 0.3190 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4797 Z= 0.148 Angle : 0.561 6.828 6484 Z= 0.288 Chirality : 0.041 0.171 721 Planarity : 0.004 0.042 747 Dihedral : 8.530 57.972 1027 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.27 % Allowed : 15.69 % Favored : 81.05 % 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 are not related in a simple way. whole: 0.11 (0.37), residues: 538 helix: 0.81 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.54 (0.54), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 241 TYR 0.020 0.001 TYR A 267 PHE 0.015 0.001 PHE A 548 TRP 0.009 0.001 TRP A 458 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4792) covalent geometry : angle 0.55770 ( 6479) SS BOND : bond 0.00112 ( 1) SS BOND : angle 1.98447 ( 2) hydrogen bonds : bond 0.04903 ( 268) hydrogen bonds : angle 4.39291 ( 780) Misc. bond : bond 0.00212 ( 3) link_NAG-ASN : bond 0.00327 ( 1) link_NAG-ASN : angle 2.63495 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.082 Fit side-chains REVERT: A 229 GLU cc_start: 0.6829 (tt0) cc_final: 0.6553 (tt0) REVERT: A 241 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7035 (mtp180) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 0.0324 time to fit residues: 2.3019 Evaluate side-chains 49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 585 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122067 restraints weight = 4928.692| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.52 r_work: 0.3196 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4797 Z= 0.150 Angle : 0.555 5.456 6484 Z= 0.286 Chirality : 0.042 0.205 721 Planarity : 0.004 0.044 747 Dihedral : 8.388 57.548 1027 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.05 % Allowed : 15.69 % Favored : 81.26 % 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 are not related in a simple way. whole: 0.16 (0.37), residues: 538 helix: 0.85 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.54 (0.54), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.020 0.001 TYR A 267 PHE 0.016 0.001 PHE A 548 TRP 0.009 0.001 TRP A 458 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4792) covalent geometry : angle 0.55148 ( 6479) SS BOND : bond 0.00155 ( 1) SS BOND : angle 1.98971 ( 2) hydrogen bonds : bond 0.04912 ( 268) hydrogen bonds : angle 4.35929 ( 780) Misc. bond : bond 0.00216 ( 3) link_NAG-ASN : bond 0.00303 ( 1) link_NAG-ASN : angle 2.59456 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.081 Fit side-chains REVERT: A 229 GLU cc_start: 0.7344 (tt0) cc_final: 0.7062 (tt0) REVERT: A 241 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7298 (mtp180) REVERT: A 444 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6715 (tp30) outliers start: 14 outliers final: 12 residues processed: 48 average time/residue: 0.0331 time to fit residues: 2.2556 Evaluate side-chains 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 585 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.144268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.122502 restraints weight = 4989.928| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.48 r_work: 0.3211 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4797 Z= 0.148 Angle : 0.557 5.456 6484 Z= 0.285 Chirality : 0.042 0.199 721 Planarity : 0.004 0.044 747 Dihedral : 8.233 58.401 1027 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.61 % Allowed : 16.12 % Favored : 81.26 % 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 are not related in a simple way. whole: 0.19 (0.37), residues: 538 helix: 0.87 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.52 (0.54), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.019 0.001 TYR A 267 PHE 0.016 0.001 PHE A 548 TRP 0.009 0.001 TRP A 458 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4792) covalent geometry : angle 0.55309 ( 6479) SS BOND : bond 0.00163 ( 1) SS BOND : angle 1.92978 ( 2) hydrogen bonds : bond 0.04859 ( 268) hydrogen bonds : angle 4.36321 ( 780) Misc. bond : bond 0.00216 ( 3) link_NAG-ASN : bond 0.00309 ( 1) link_NAG-ASN : angle 2.51994 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.081 Fit side-chains REVERT: A 229 GLU cc_start: 0.6799 (tt0) cc_final: 0.6523 (tt0) REVERT: A 241 ARG cc_start: 0.7704 (mtp85) cc_final: 0.6997 (mtp180) REVERT: A 444 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6163 (tp30) outliers start: 12 outliers final: 11 residues processed: 47 average time/residue: 0.0335 time to fit residues: 2.2253 Evaluate side-chains 49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 585 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 0.0070 chunk 17 optimal weight: 0.0970 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.150649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.127717 restraints weight = 4820.878| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.58 r_work: 0.3271 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4797 Z= 0.113 Angle : 0.521 6.890 6484 Z= 0.267 Chirality : 0.040 0.196 721 Planarity : 0.004 0.044 747 Dihedral : 7.620 59.501 1027 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.40 % Allowed : 16.34 % Favored : 81.26 % 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 are not related in a simple way. whole: 0.49 (0.38), residues: 538 helix: 1.14 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.48 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.014 0.001 TYR A 267 PHE 0.014 0.001 PHE A 548 TRP 0.011 0.001 TRP A 458 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4792) covalent geometry : angle 0.51826 ( 6479) SS BOND : bond 0.00066 ( 1) SS BOND : angle 1.48928 ( 2) hydrogen bonds : bond 0.04341 ( 268) hydrogen bonds : angle 4.16961 ( 780) Misc. bond : bond 0.00149 ( 3) link_NAG-ASN : bond 0.00357 ( 1) link_NAG-ASN : angle 2.40681 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.081 Fit side-chains REVERT: A 241 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7163 (mtp180) REVERT: A 377 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7100 (t80) REVERT: A 444 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6238 (tp30) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.0329 time to fit residues: 2.3349 Evaluate side-chains 47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 585 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.2038 > 50: distance: 67 - 72: 9.465 distance: 72 - 73: 40.083 distance: 73 - 74: 37.985 distance: 73 - 76: 49.855 distance: 74 - 75: 8.794 distance: 74 - 78: 31.077 distance: 75 - 107: 18.240 distance: 76 - 77: 32.653 distance: 78 - 79: 28.158 distance: 79 - 80: 16.578 distance: 79 - 82: 23.098 distance: 80 - 81: 10.507 distance: 80 - 90: 5.300 distance: 81 - 112: 12.853 distance: 82 - 83: 16.672 distance: 83 - 84: 11.279 distance: 83 - 85: 9.759 distance: 84 - 86: 8.680 distance: 85 - 87: 7.736 distance: 86 - 88: 5.384 distance: 88 - 89: 3.766 distance: 90 - 91: 27.369 distance: 91 - 92: 44.162 distance: 91 - 94: 45.449 distance: 92 - 93: 32.985 distance: 92 - 99: 35.853 distance: 93 - 120: 20.694 distance: 94 - 95: 35.499 distance: 95 - 96: 41.539 distance: 96 - 97: 37.258 distance: 96 - 98: 18.921 distance: 99 - 100: 32.764 distance: 100 - 101: 41.044 distance: 100 - 103: 28.452 distance: 101 - 102: 34.503 distance: 101 - 107: 37.633 distance: 102 - 127: 25.764 distance: 103 - 104: 18.553 distance: 104 - 105: 33.263 distance: 104 - 106: 44.098 distance: 107 - 108: 16.016 distance: 108 - 109: 39.536 distance: 108 - 111: 23.077 distance: 109 - 110: 35.281 distance: 109 - 112: 33.730 distance: 110 - 134: 29.877 distance: 112 - 113: 10.881 distance: 113 - 114: 36.924 distance: 113 - 116: 9.146 distance: 114 - 115: 29.928 distance: 114 - 120: 30.353 distance: 115 - 140: 49.482 distance: 116 - 117: 14.834 distance: 117 - 118: 11.045 distance: 117 - 119: 16.491 distance: 120 - 121: 9.699 distance: 121 - 122: 30.194 distance: 121 - 124: 29.299 distance: 122 - 123: 24.889 distance: 122 - 127: 37.862 distance: 123 - 147: 11.322 distance: 124 - 125: 24.187 distance: 124 - 126: 19.966 distance: 127 - 128: 29.762 distance: 128 - 129: 53.364 distance: 128 - 131: 25.294 distance: 129 - 130: 42.377 distance: 129 - 134: 28.798 distance: 131 - 132: 13.867 distance: 131 - 133: 12.161 distance: 134 - 135: 18.438 distance: 135 - 136: 47.604 distance: 135 - 138: 21.421 distance: 136 - 137: 45.864 distance: 136 - 140: 46.640 distance: 137 - 160: 13.327 distance: 138 - 139: 40.340 distance: 140 - 141: 56.204 distance: 141 - 142: 50.865 distance: 141 - 144: 30.258 distance: 142 - 143: 49.810 distance: 142 - 147: 21.794 distance: 143 - 166: 26.795 distance: 144 - 145: 5.286 distance: 144 - 146: 16.233 distance: 145 - 199: 10.145