Starting phenix.real_space_refine on Thu Jul 2 06:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfq_61436/07_2026/9jfq_61436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfq_61436/07_2026/9jfq_61436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jfq_61436/07_2026/9jfq_61436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfq_61436/07_2026/9jfq_61436.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfq_61436/07_2026/9jfq_61436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfq_61436/07_2026/9jfq_61436.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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 P 165 5.49 5 S 19 5.16 5 C 3980 2.51 5 N 1356 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7281 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3787 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 27, 'TRANS': 450} Chain: "C" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2236 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 56, 'rna3p_pyr': 39} Link IDs: {'rna2p': 9, 'rna3p': 94} Chain breaks: 2 Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 811 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Time building chain proxies: 1.41, per 1000 atoms: 0.19 Number of scatterers: 7281 At special positions: 0 Unit cell: (108.25, 97.425, 113.662, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 165 15.00 O 1761 8.00 N 1356 7.00 C 3980 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: 0.67 Conformation dependent library (CDL) restraints added in 254.2 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 39.5% alpha, 7.1% beta 55 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.599A pdb=" N ARG A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.577A pdb=" N ILE A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.657A pdb=" N ASP A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.698A pdb=" N ASP A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 374 removed outlier: 3.507A pdb=" N GLY A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 414 removed outlier: 4.006A pdb=" N PHE A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.972A pdb=" N ASN A 446 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 481 removed outlier: 3.636A pdb=" N ASN A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.700A pdb=" N ASN A 8 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.753A pdb=" N MET A 19 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS A 220 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR A 206 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 145 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.182A pdb=" N GLU A 248 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 377 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.727A pdb=" N ALA A 260 " --> pdb=" O TYR A 268 " (cutoff:3.500A) 144 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.83 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: 1482 1.33 - 1.45: 2619 1.45 - 1.58: 3324 1.58 - 1.70: 325 1.70 - 1.82: 30 Bond restraints: 7780 Sorted by residual: bond pdb=" C1' DT G 19 " pdb=" N1 DT G 19 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C3' DA G 28 " pdb=" C2' DA G 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG G 25 " pdb=" C2' DG G 25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" C1' DC C 14 " pdb=" N1 DC C 14 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.72e+00 bond pdb=" C3' DC C 11 " pdb=" C2' DC C 11 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.63e+00 ... (remaining 7775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 10722 1.56 - 3.12: 508 3.12 - 4.68: 47 4.68 - 6.24: 8 6.24 - 7.80: 5 Bond angle restraints: 11290 Sorted by residual: angle pdb=" N ILE A 259 " pdb=" CA ILE A 259 " pdb=" C ILE A 259 " ideal model delta sigma weight residual 113.71 105.91 7.80 9.50e-01 1.11e+00 6.73e+01 angle pdb=" C4' U F 23 " pdb=" C3' U F 23 " pdb=" O3' U F 23 " ideal model delta sigma weight residual 109.40 116.05 -6.65 1.50e+00 4.44e-01 1.96e+01 angle pdb=" N1 C F 20 " pdb=" C2 C F 20 " pdb=" O2 C F 20 " ideal model delta sigma weight residual 118.90 121.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O2 C F 20 " pdb=" C2 C F 20 " pdb=" N3 C F 20 " ideal model delta sigma weight residual 121.90 118.86 3.04 7.00e-01 2.04e+00 1.89e+01 angle pdb=" O4' DT G 9 " pdb=" C4' DT G 9 " pdb=" C3' DT G 9 " ideal model delta sigma weight residual 106.00 103.40 2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 11285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 4021 34.29 - 68.59: 594 68.59 - 102.88: 49 102.88 - 137.18: 7 137.18 - 171.47: 3 Dihedral angle restraints: 4674 sinusoidal: 3273 harmonic: 1401 Sorted by residual: dihedral pdb=" C5' G F 77 " pdb=" C4' G F 77 " pdb=" C3' G F 77 " pdb=" O3' G F 77 " ideal model delta sinusoidal sigma weight residual 147.00 103.49 43.51 1 8.00e+00 1.56e-02 4.12e+01 dihedral pdb=" O4' G F 77 " pdb=" C4' G F 77 " pdb=" C3' G F 77 " pdb=" C2' G F 77 " ideal model delta sinusoidal sigma weight residual 24.00 -12.48 36.48 1 8.00e+00 1.56e-02 2.94e+01 dihedral pdb=" CA SER A 142 " pdb=" C SER A 142 " pdb=" N PHE A 143 " pdb=" CA PHE A 143 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 4671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1095 0.052 - 0.105: 193 0.105 - 0.157: 31 0.157 - 0.209: 7 0.209 - 0.261: 3 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C3' U F 23 " pdb=" C4' U F 23 " pdb=" O3' U F 23 " pdb=" C2' U F 23 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' G F 77 " pdb=" C4' G F 77 " pdb=" O3' G F 77 " pdb=" C2' G F 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" P A F 78 " pdb=" OP1 A F 78 " pdb=" OP2 A F 78 " pdb=" O5' A F 78 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1326 not shown) Planarity restraints: 845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 173 " 0.025 2.00e-02 2.50e+03 1.15e-02 3.63e+00 pdb=" N9 A F 173 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A F 173 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A F 173 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A F 173 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A F 173 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A F 173 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A F 173 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A F 173 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A F 173 " -0.001 2.00e-02 2.50e+03 pdb=" C4 A F 173 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F 20 " 0.019 2.00e-02 2.50e+03 1.15e-02 2.99e+00 pdb=" N1 C F 20 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C F 20 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C F 20 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C F 20 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C F 20 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C F 20 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C F 20 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C F 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 326 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO A 327 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.024 5.00e-02 4.00e+02 ... (remaining 842 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 415 2.70 - 3.25: 7062 3.25 - 3.80: 13621 3.80 - 4.35: 16700 4.35 - 4.90: 24092 Nonbonded interactions: 61890 Sorted by model distance: nonbonded pdb=" O2' A F 137 " pdb=" O4' A F 138 " model vdw 2.146 3.040 nonbonded pdb=" O2' A F 131 " pdb=" OP2 U F 132 " model vdw 2.203 3.040 nonbonded pdb=" NE2 GLN A 32 " pdb=" O LYS A 168 " model vdw 2.212 3.120 nonbonded pdb=" NZ LYS A 174 " pdb=" OP2 G F 160 " model vdw 2.222 3.120 nonbonded pdb=" O2 DT C 15 " pdb=" N2 G F 176 " model vdw 2.223 2.496 ... (remaining 61885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.060 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.010 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 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 0.074 7780 Z= 0.345 Angle : 0.710 7.795 11290 Z= 0.581 Chirality : 0.043 0.261 1329 Planarity : 0.005 0.043 845 Dihedral : 25.409 171.470 3764 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.25 % Allowed : 0.99 % Favored : 98.77 % 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: -1.62 (0.38), residues: 476 helix: -0.04 (0.38), residues: 184 sheet: -3.46 (0.58), residues: 60 loop : -1.16 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 176 TYR 0.024 0.002 TYR A 364 PHE 0.024 0.002 PHE A 143 TRP 0.013 0.002 TRP A 69 HIS 0.008 0.002 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.34 ( 7780) covalent geometry : angle 0.71023 / 0.58 (11290) hydrogen bonds : bond 0.13532 / 8.24 ( 281) hydrogen bonds : angle 5.56350 / 4.00 ( 672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 354 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7122 (ttp80) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.1176 time to fit residues: 8.8742 Evaluate side-chains 46 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 179 ASN A 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.221619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.189543 restraints weight = 13155.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.191442 restraints weight = 25324.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.192394 restraints weight = 14603.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.192426 restraints weight = 10780.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.192804 restraints weight = 10158.036| |-----------------------------------------------------------------------------| r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 7780 Z= 0.434 Angle : 0.988 11.828 11290 Z= 0.538 Chirality : 0.059 0.387 1329 Planarity : 0.008 0.070 845 Dihedral : 27.705 169.020 2805 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 4.20 % Allowed : 10.37 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.64 (0.36), residues: 476 helix: -0.78 (0.36), residues: 191 sheet: -3.84 (0.63), residues: 48 loop : -2.09 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 354 TYR 0.062 0.005 TYR A 412 PHE 0.060 0.005 PHE A 143 TRP 0.017 0.004 TRP A 114 HIS 0.021 0.005 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.43 ( 7780) covalent geometry : angle 0.98754 / 0.54 (11290) hydrogen bonds : bond 0.11225 / 7.27 ( 281) hydrogen bonds : angle 5.21035 / 3.69 ( 672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.215 Fit side-chains REVERT: A 49 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6277 (t-90) REVERT: A 152 ILE cc_start: 0.5811 (mt) cc_final: 0.5379 (mt) REVERT: A 223 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7540 (m-10) REVERT: A 300 ARG cc_start: 0.3906 (OUTLIER) cc_final: 0.3370 (ttm110) REVERT: A 354 ARG cc_start: 0.7038 (ttp-170) cc_final: 0.6600 (ttp80) outliers start: 17 outliers final: 9 residues processed: 57 average time/residue: 0.1095 time to fit residues: 8.0175 Evaluate side-chains 53 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 392 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 40.0000 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.216583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.176573 restraints weight = 12782.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.175694 restraints weight = 15436.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.177158 restraints weight = 11967.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.180749 restraints weight = 8029.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.180719 restraints weight = 5958.352| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7780 Z= 0.207 Angle : 0.710 9.647 11290 Z= 0.400 Chirality : 0.046 0.245 1329 Planarity : 0.006 0.044 845 Dihedral : 27.671 172.298 2805 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.46 % Allowed : 12.84 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.09 (0.37), residues: 476 helix: -0.29 (0.37), residues: 181 sheet: -3.80 (0.60), residues: 48 loop : -1.70 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 393 TYR 0.035 0.003 TYR A 412 PHE 0.024 0.002 PHE A 143 TRP 0.012 0.002 TRP A 235 HIS 0.020 0.003 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 ( 7780) covalent geometry : angle 0.71026 / 0.40 (11290) hydrogen bonds : bond 0.07944 / 5.19 ( 281) hydrogen bonds : angle 4.57626 / 3.28 ( 672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 361 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.6055 (m-30) outliers start: 14 outliers final: 5 residues processed: 49 average time/residue: 0.0993 time to fit residues: 6.4593 Evaluate side-chains 47 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 392 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.220246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.188480 restraints weight = 13318.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.190235 restraints weight = 24999.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.190987 restraints weight = 15256.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.191010 restraints weight = 11564.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.191393 restraints weight = 10369.936| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 7780 Z= 0.420 Angle : 0.962 12.133 11290 Z= 0.526 Chirality : 0.058 0.338 1329 Planarity : 0.008 0.063 845 Dihedral : 27.796 156.766 2801 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 5.43 % Allowed : 15.06 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.73 (0.36), residues: 476 helix: -0.93 (0.35), residues: 185 sheet: -4.29 (0.65), residues: 43 loop : -2.01 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 176 TYR 0.044 0.004 TYR A 412 PHE 0.054 0.004 PHE A 143 TRP 0.015 0.004 TRP A 80 HIS 0.009 0.003 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.42 ( 7780) covalent geometry : angle 0.96241 / 0.53 (11290) hydrogen bonds : bond 0.11062 / 7.17 ( 281) hydrogen bonds : angle 5.20709 / 3.67 ( 672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.238 Fit side-chains REVERT: A 49 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6194 (t-90) REVERT: A 152 ILE cc_start: 0.5756 (mt) cc_final: 0.5310 (mt) REVERT: A 173 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6324 (mt) REVERT: A 176 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7687 (tpt90) REVERT: A 286 ARG cc_start: 0.7438 (ptt90) cc_final: 0.7099 (ptt90) outliers start: 22 outliers final: 14 residues processed: 55 average time/residue: 0.0887 time to fit residues: 6.6683 Evaluate side-chains 55 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 419 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.221275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.187148 restraints weight = 13168.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.189356 restraints weight = 22964.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.190122 restraints weight = 14425.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.190241 restraints weight = 10171.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.190744 restraints weight = 9394.702| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 7780 Z= 0.369 Angle : 0.891 10.664 11290 Z= 0.488 Chirality : 0.056 0.303 1329 Planarity : 0.007 0.058 845 Dihedral : 27.758 144.632 2801 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 5.19 % Allowed : 17.53 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.78 (0.36), residues: 476 helix: -0.94 (0.35), residues: 186 sheet: -4.22 (0.64), residues: 43 loop : -2.10 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 176 TYR 0.039 0.004 TYR A 412 PHE 0.047 0.003 PHE A 143 TRP 0.016 0.003 TRP A 235 HIS 0.014 0.003 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.37 ( 7780) covalent geometry : angle 0.89061 / 0.49 (11290) hydrogen bonds : bond 0.10125 / 6.53 ( 281) hydrogen bonds : angle 5.05505 / 3.56 ( 672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6249 (t-90) REVERT: A 173 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6246 (mt) REVERT: A 176 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7646 (tpt90) REVERT: A 286 ARG cc_start: 0.7606 (ptt90) cc_final: 0.7262 (ptt90) outliers start: 21 outliers final: 10 residues processed: 56 average time/residue: 0.0647 time to fit residues: 4.9799 Evaluate side-chains 51 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.225058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.189793 restraints weight = 13232.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.190278 restraints weight = 21392.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.191629 restraints weight = 17633.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.192462 restraints weight = 11096.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.192866 restraints weight = 10140.699| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7780 Z= 0.242 Angle : 0.757 9.888 11290 Z= 0.420 Chirality : 0.049 0.258 1329 Planarity : 0.006 0.050 845 Dihedral : 27.623 143.980 2801 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.20 % Allowed : 19.26 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.43 (0.37), residues: 476 helix: -0.63 (0.36), residues: 187 sheet: -4.09 (0.65), residues: 43 loop : -1.91 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 393 TYR 0.031 0.003 TYR A 412 PHE 0.032 0.003 PHE A 143 TRP 0.016 0.002 TRP A 235 HIS 0.019 0.003 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 ( 7780) covalent geometry : angle 0.75652 / 0.42 (11290) hydrogen bonds : bond 0.08478 / 5.49 ( 281) hydrogen bonds : angle 4.68063 / 3.31 ( 672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.105 Fit side-chains REVERT: A 49 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.5906 (t-90) REVERT: A 286 ARG cc_start: 0.7665 (ptt90) cc_final: 0.7320 (ptt90) outliers start: 17 outliers final: 8 residues processed: 53 average time/residue: 0.0712 time to fit residues: 5.0706 Evaluate side-chains 47 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 412 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.9429 > 50: distance: 89 - 96: 29.046 distance: 96 - 97: 45.375 distance: 97 - 98: 41.090 distance: 97 - 100: 38.755 distance: 98 - 99: 18.433 distance: 98 - 101: 56.223 distance: 102 - 103: 41.465 distance: 102 - 105: 39.656 distance: 103 - 104: 55.967 distance: 103 - 112: 40.996 distance: 107 - 108: 56.843 distance: 108 - 109: 39.405 distance: 109 - 111: 41.307 distance: 112 - 113: 39.170 distance: 114 - 115: 55.335 distance: 114 - 116: 57.234 distance: 117 - 118: 39.435 distance: 120 - 121: 40.398 distance: 121 - 122: 39.520 distance: 123 - 125: 39.686 distance: 127 - 128: 40.502 distance: 128 - 129: 56.948 distance: 128 - 131: 39.373 distance: 129 - 130: 55.659 distance: 132 - 134: 41.153 distance: 136 - 137: 56.788 distance: 136 - 139: 41.251 distance: 137 - 146: 40.465 distance: 139 - 140: 38.697 distance: 140 - 141: 39.121 distance: 143 - 144: 40.869 distance: 143 - 145: 39.744 distance: 147 - 148: 40.868 distance: 147 - 150: 55.826 distance: 148 - 149: 40.504 distance: 148 - 155: 40.361 distance: 151 - 152: 56.364 distance: 152 - 153: 56.128 distance: 153 - 154: 41.023 distance: 155 - 156: 40.573 distance: 159 - 161: 69.585 distance: 163 - 249: 32.599 distance: 164 - 165: 44.732 distance: 164 - 167: 41.298 distance: 165 - 166: 43.799 distance: 165 - 177: 31.372 distance: 166 - 246: 33.484 distance: 167 - 168: 56.412 distance: 168 - 169: 57.422 distance: 168 - 170: 38.620 distance: 170 - 173: 41.208 distance: 171 - 172: 40.089 distance: 172 - 174: 40.532 distance: 173 - 175: 42.974 distance: 174 - 176: 40.233 distance: 175 - 176: 16.690 distance: 177 - 178: 26.129 distance: 178 - 179: 39.277 distance: 178 - 181: 55.501 distance: 179 - 188: 34.776 distance: 181 - 182: 40.521 distance: 182 - 184: 56.146 distance: 185 - 187: 40.727 distance: 186 - 187: 39.353