Starting phenix.real_space_refine on Tue Feb 3 23:45:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uk5_26575/02_2026/7uk5_26575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uk5_26575/02_2026/7uk5_26575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2026/7uk5_26575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2026/7uk5_26575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2026/7uk5_26575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2026/7uk5_26575.map" } resolution = 2.76 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= 0.005 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.46, per 1000 atoms: 0.18 Number of scatterers: 8000 At special positions: 0 Unit cell: (116.466, 116.466, 78.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 187.5 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 182 through 205 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 Processing helix chain 'C' and resid 401 through 424 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.096A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 Processing helix chain 'D' and resid 401 through 424 633 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.69 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: 2436 1.34 - 1.46: 2009 1.46 - 1.58: 3655 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG D 418 " pdb=" CA ARG D 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG B 418 " pdb=" CA ARG B 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 3.96e+00 bond pdb=" C GLN C 417 " pdb=" N ARG C 418 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.98e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 10372 1.00 - 1.99: 585 1.99 - 2.99: 115 2.99 - 3.98: 33 3.98 - 4.98: 19 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CA TYR C 188 " pdb=" CB TYR C 188 " pdb=" CG TYR C 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.67e+00 angle pdb=" N THR B 182 " pdb=" CA THR B 182 " pdb=" C THR B 182 " ideal model delta sigma weight residual 113.41 110.51 2.90 1.22e+00 6.72e-01 5.66e+00 angle pdb=" CA TYR D 188 " pdb=" CB TYR D 188 " pdb=" CG TYR D 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.64e+00 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 113.41 110.53 2.88 1.22e+00 6.72e-01 5.58e+00 angle pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4400 17.87 - 35.73: 336 35.73 - 53.60: 44 53.60 - 71.47: 4 71.47 - 89.34: 8 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CG ARG D 411 " pdb=" CD ARG D 411 " pdb=" NE ARG D 411 " pdb=" CZ ARG D 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.89 -43.11 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG C 411 " pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " pdb=" CZ ARG C 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG B 411 " pdb=" CD ARG B 411 " pdb=" NE ARG B 411 " pdb=" CZ ARG B 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 702 0.027 - 0.055: 352 0.055 - 0.082: 199 0.082 - 0.110: 41 0.110 - 0.137: 26 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CB VAL B 297 " pdb=" CA VAL B 297 " pdb=" CG1 VAL B 297 " pdb=" CG2 VAL B 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " 0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLN B 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN B 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 418 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 417 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN A 417 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN A 417 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 418 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 417 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN C 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN C 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 418 " 0.019 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 810 2.74 - 3.34: 10002 3.34 - 3.94: 15630 3.94 - 4.54: 21328 4.54 - 5.14: 32150 Nonbonded interactions: 79920 Sorted by model distance: nonbonded pdb=" OE2 GLU C 205 " pdb=" NH2 ARG C 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU A 205 " pdb=" NH2 ARG A 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 296 " model vdw 2.139 3.120 nonbonded pdb=" O PHE D 257 " pdb=" OG SER D 260 " model vdw 2.343 3.040 ... (remaining 79915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.004 0.029 8188 Z= 0.197 Angle : 0.581 4.978 11124 Z= 0.349 Chirality : 0.042 0.137 1320 Planarity : 0.006 0.049 1360 Dihedral : 12.964 89.336 2840 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.44 (0.27), residues: 1028 helix: 1.57 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -1.21 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 418 TYR 0.020 0.002 TYR D 188 PHE 0.010 0.001 PHE B 289 TRP 0.004 0.001 TRP B 172 HIS 0.001 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8188) covalent geometry : angle 0.58135 (11124) hydrogen bonds : bond 0.12175 ( 633) hydrogen bonds : angle 5.00289 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.4374 time to fit residues: 50.2497 Evaluate side-chains 96 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.166659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115978 restraints weight = 8638.088| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.89 r_work: 0.3240 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8188 Z= 0.163 Angle : 0.509 4.398 11124 Z= 0.287 Chirality : 0.041 0.130 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.844 16.239 1148 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 6.64 % Favored : 91.47 % 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: 2.14 (0.27), residues: 1028 helix: 1.91 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -0.29 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 256 TYR 0.018 0.002 TYR A 188 PHE 0.013 0.001 PHE D 257 TRP 0.007 0.001 TRP A 362 HIS 0.001 0.000 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8188) covalent geometry : angle 0.50915 (11124) hydrogen bonds : bond 0.04543 ( 633) hydrogen bonds : angle 3.96879 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.224 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.4603 time to fit residues: 52.8382 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.0030 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.168776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117974 restraints weight = 8596.342| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.92 r_work: 0.3275 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8188 Z= 0.124 Angle : 0.472 4.500 11124 Z= 0.261 Chirality : 0.039 0.121 1320 Planarity : 0.005 0.049 1360 Dihedral : 3.622 14.426 1148 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.95 % Allowed : 9.24 % Favored : 89.81 % 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: 2.57 (0.28), residues: 1028 helix: 2.18 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.00 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 418 TYR 0.018 0.001 TYR A 188 PHE 0.011 0.001 PHE A 257 TRP 0.005 0.001 TRP A 362 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8188) covalent geometry : angle 0.47237 (11124) hydrogen bonds : bond 0.04093 ( 633) hydrogen bonds : angle 3.83401 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.257 Fit side-chains REVERT: A 347 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7903 (ptmm) REVERT: B 347 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7910 (ptmm) REVERT: D 347 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7886 (ptmm) outliers start: 8 outliers final: 8 residues processed: 114 average time/residue: 0.4518 time to fit residues: 55.0156 Evaluate side-chains 110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.163697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112335 restraints weight = 8742.723| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.94 r_work: 0.3210 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 8188 Z= 0.264 Angle : 0.575 4.644 11124 Z= 0.317 Chirality : 0.045 0.139 1320 Planarity : 0.005 0.046 1360 Dihedral : 4.009 16.877 1148 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.25 % Allowed : 9.00 % Favored : 88.74 % 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: 2.04 (0.27), residues: 1028 helix: 1.82 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.28 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 254 TYR 0.019 0.002 TYR A 188 PHE 0.012 0.002 PHE B 257 TRP 0.008 0.002 TRP D 172 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 8188) covalent geometry : angle 0.57509 (11124) hydrogen bonds : bond 0.05033 ( 633) hydrogen bonds : angle 3.97955 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.346 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 111 average time/residue: 0.5116 time to fit residues: 60.5783 Evaluate side-chains 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.165848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115334 restraints weight = 8689.130| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.89 r_work: 0.3233 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8188 Z= 0.165 Angle : 0.499 4.560 11124 Z= 0.278 Chirality : 0.041 0.126 1320 Planarity : 0.005 0.047 1360 Dihedral : 3.814 15.806 1148 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.01 % Allowed : 10.55 % Favored : 87.44 % 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 are not related in a simple way. whole: 2.32 (0.28), residues: 1028 helix: 2.02 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.18 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 418 TYR 0.016 0.002 TYR B 188 PHE 0.011 0.001 PHE D 257 TRP 0.006 0.001 TRP C 172 HIS 0.001 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8188) covalent geometry : angle 0.49935 (11124) hydrogen bonds : bond 0.04388 ( 633) hydrogen bonds : angle 3.89201 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.272 Fit side-chains REVERT: A 396 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5378 (tm) REVERT: B 396 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5367 (tm) REVERT: C 396 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5360 (tm) REVERT: D 396 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5386 (tm) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 0.4731 time to fit residues: 51.9422 Evaluate side-chains 106 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.168540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118572 restraints weight = 8634.140| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.88 r_work: 0.3276 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8188 Z= 0.123 Angle : 0.468 4.453 11124 Z= 0.258 Chirality : 0.039 0.119 1320 Planarity : 0.005 0.050 1360 Dihedral : 3.583 14.195 1148 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.78 % Allowed : 11.85 % Favored : 86.37 % 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: 2.59 (0.28), residues: 1028 helix: 2.20 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.016 0.001 TYR B 188 PHE 0.009 0.001 PHE B 257 TRP 0.004 0.001 TRP B 172 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8188) covalent geometry : angle 0.46757 (11124) hydrogen bonds : bond 0.03986 ( 633) hydrogen bonds : angle 3.80803 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.187 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 103 average time/residue: 0.4743 time to fit residues: 51.8879 Evaluate side-chains 103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 0.0030 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 70 optimal weight: 0.0040 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.168598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118638 restraints weight = 8745.854| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.89 r_work: 0.3276 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8188 Z= 0.124 Angle : 0.469 4.491 11124 Z= 0.258 Chirality : 0.039 0.118 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.488 13.292 1148 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.07 % Allowed : 13.63 % Favored : 85.31 % 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: 2.65 (0.28), residues: 1028 helix: 2.24 (0.19), residues: 804 sheet: None (None), residues: 0 loop : 0.01 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 299 TYR 0.015 0.001 TYR C 188 PHE 0.009 0.001 PHE A 257 TRP 0.004 0.001 TRP B 362 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8188) covalent geometry : angle 0.46931 (11124) hydrogen bonds : bond 0.03970 ( 633) hydrogen bonds : angle 3.78210 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.204 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 103 average time/residue: 0.4520 time to fit residues: 49.6083 Evaluate side-chains 103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118197 restraints weight = 8654.851| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.90 r_work: 0.3265 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8188 Z= 0.141 Angle : 0.488 4.792 11124 Z= 0.267 Chirality : 0.040 0.121 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.534 13.845 1148 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.95 % Allowed : 12.80 % Favored : 86.26 % 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: 2.62 (0.28), residues: 1028 helix: 2.22 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.02 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 418 TYR 0.014 0.001 TYR C 188 PHE 0.009 0.001 PHE B 257 TRP 0.006 0.001 TRP A 362 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8188) covalent geometry : angle 0.48805 (11124) hydrogen bonds : bond 0.04091 ( 633) hydrogen bonds : angle 3.82014 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.306 Fit side-chains REVERT: B 279 MET cc_start: 0.5073 (mtm) cc_final: 0.4523 (ptm) REVERT: C 279 MET cc_start: 0.5064 (mtm) cc_final: 0.4514 (ptm) REVERT: D 279 MET cc_start: 0.5073 (mtm) cc_final: 0.4521 (ptm) outliers start: 8 outliers final: 8 residues processed: 104 average time/residue: 0.5035 time to fit residues: 55.8163 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.168657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118539 restraints weight = 8586.459| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.90 r_work: 0.3269 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8188 Z= 0.136 Angle : 0.485 4.865 11124 Z= 0.266 Chirality : 0.039 0.120 1320 Planarity : 0.005 0.053 1360 Dihedral : 3.517 13.723 1148 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.42 % Allowed : 12.80 % Favored : 85.78 % 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: 2.61 (0.28), residues: 1028 helix: 2.24 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.09 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 299 TYR 0.013 0.001 TYR C 188 PHE 0.009 0.001 PHE D 257 TRP 0.005 0.001 TRP A 172 HIS 0.001 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8188) covalent geometry : angle 0.48492 (11124) hydrogen bonds : bond 0.04062 ( 633) hydrogen bonds : angle 3.83174 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.323 Fit side-chains REVERT: A 279 MET cc_start: 0.5087 (mtm) cc_final: 0.4557 (ptm) REVERT: B 279 MET cc_start: 0.5153 (mtm) cc_final: 0.4617 (ptm) REVERT: C 279 MET cc_start: 0.5145 (mtm) cc_final: 0.4611 (ptm) REVERT: D 279 MET cc_start: 0.5155 (mtm) cc_final: 0.4621 (ptm) outliers start: 12 outliers final: 12 residues processed: 103 average time/residue: 0.5367 time to fit residues: 58.8303 Evaluate side-chains 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.169019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118980 restraints weight = 8623.193| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.90 r_work: 0.3274 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.131 Angle : 0.486 5.147 11124 Z= 0.266 Chirality : 0.039 0.119 1320 Planarity : 0.005 0.053 1360 Dihedral : 3.484 13.605 1148 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.66 % Allowed : 13.03 % Favored : 85.31 % 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: 2.63 (0.28), residues: 1028 helix: 2.25 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.10 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 254 TYR 0.012 0.001 TYR C 188 PHE 0.009 0.001 PHE D 257 TRP 0.005 0.001 TRP A 362 HIS 0.001 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8188) covalent geometry : angle 0.48573 (11124) hydrogen bonds : bond 0.04038 ( 633) hydrogen bonds : angle 3.84159 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.211 Fit side-chains REVERT: A 279 MET cc_start: 0.5192 (mtm) cc_final: 0.4677 (ptm) REVERT: B 279 MET cc_start: 0.5185 (mtm) cc_final: 0.4723 (ptm) REVERT: C 279 MET cc_start: 0.5182 (mtm) cc_final: 0.4721 (ptm) REVERT: D 279 MET cc_start: 0.5190 (mtm) cc_final: 0.4728 (ptm) outliers start: 14 outliers final: 12 residues processed: 103 average time/residue: 0.5280 time to fit residues: 57.9261 Evaluate side-chains 105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 50.4739 > 50: distance: 17 - 39: 7.713 distance: 21 - 46: 16.110 distance: 28 - 31: 23.217 distance: 29 - 57: 13.449 distance: 31 - 32: 20.646 distance: 32 - 33: 34.954 distance: 32 - 35: 20.852 distance: 33 - 34: 15.831 distance: 33 - 39: 10.600 distance: 34 - 69: 27.622 distance: 36 - 37: 33.275 distance: 36 - 38: 35.162 distance: 39 - 40: 11.807 distance: 40 - 41: 10.823 distance: 40 - 43: 17.169 distance: 41 - 42: 14.511 distance: 41 - 46: 5.703 distance: 42 - 81: 19.266 distance: 43 - 44: 14.929 distance: 43 - 45: 19.397 distance: 46 - 47: 8.392 distance: 47 - 50: 11.026 distance: 48 - 49: 11.585 distance: 48 - 57: 18.270 distance: 49 - 88: 7.687 distance: 50 - 51: 4.973 distance: 51 - 52: 5.897 distance: 52 - 54: 11.156 distance: 53 - 55: 6.458 distance: 54 - 56: 5.994 distance: 55 - 56: 6.061 distance: 57 - 58: 10.171 distance: 58 - 59: 17.913 distance: 58 - 61: 17.018 distance: 59 - 60: 14.100 distance: 59 - 69: 6.764 distance: 60 - 95: 40.797 distance: 61 - 62: 10.850 distance: 62 - 63: 9.781 distance: 62 - 64: 4.324 distance: 63 - 65: 11.052 distance: 64 - 66: 4.297 distance: 65 - 67: 8.516 distance: 66 - 67: 8.525 distance: 67 - 68: 4.836 distance: 69 - 70: 11.580 distance: 70 - 73: 11.143 distance: 71 - 72: 4.332 distance: 71 - 81: 33.651 distance: 72 - 99: 33.944 distance: 73 - 74: 9.121 distance: 74 - 76: 9.515 distance: 75 - 77: 10.224 distance: 76 - 78: 8.704 distance: 77 - 79: 9.807 distance: 79 - 80: 11.015 distance: 81 - 82: 8.556 distance: 82 - 83: 23.081 distance: 82 - 85: 28.031 distance: 83 - 84: 7.649 distance: 83 - 88: 7.797 distance: 84 - 110: 35.973 distance: 85 - 86: 35.539 distance: 85 - 87: 21.203 distance: 88 - 89: 11.798 distance: 89 - 90: 11.099 distance: 89 - 92: 12.134 distance: 90 - 91: 10.881 distance: 90 - 95: 8.511 distance: 91 - 121: 21.038 distance: 92 - 93: 13.471 distance: 92 - 94: 19.855 distance: 95 - 96: 15.915 distance: 96 - 97: 9.718 distance: 97 - 98: 6.767 distance: 97 - 99: 19.726 distance: 98 - 129: 24.333 distance: 99 - 100: 16.990 distance: 100 - 101: 20.799 distance: 100 - 103: 12.159 distance: 101 - 102: 16.590 distance: 101 - 110: 15.361 distance: 102 - 134: 35.649 distance: 103 - 104: 10.144 distance: 104 - 105: 5.217 distance: 104 - 106: 5.696 distance: 105 - 107: 10.182 distance: 106 - 108: 7.138 distance: 108 - 109: 5.466 distance: 110 - 111: 15.340 distance: 111 - 112: 9.446 distance: 111 - 114: 8.092 distance: 112 - 113: 9.638 distance: 112 - 121: 12.815 distance: 113 - 141: 20.438 distance: 114 - 115: 8.346 distance: 115 - 116: 10.171 distance: 115 - 117: 18.887 distance: 116 - 118: 19.220 distance: 117 - 119: 15.818 distance: 118 - 120: 23.101 distance: 119 - 120: 16.651