Starting phenix.real_space_refine on Thu Jul 2 19:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zi9_74266/07_2026/9zi9_74266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zi9_74266/07_2026/9zi9_74266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zi9_74266/07_2026/9zi9_74266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zi9_74266/07_2026/9zi9_74266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zi9_74266/07_2026/9zi9_74266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zi9_74266/07_2026/9zi9_74266.map" } resolution = 3.2 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 417 5.49 5 Mg 33 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 9944 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 26, 'rna2p_pyr': 18, 'rna3p_pur': 217, 'rna3p_pyr': 156} Link IDs: {'rna2p': 44, 'rna3p': 372} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Unusual residues: {' MG': 33} Classifications: {'undetermined': 33, 'water': 2} Link IDs: {None: 34} Time building chain proxies: 1.99, per 1000 atoms: 0.20 Number of scatterers: 9944 At special positions: 0 Unit cell: (101.748, 163.968, 146.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 3 16.00 P 417 15.00 Mg 33 11.99 O 3053 8.00 N 1834 7.00 C 4604 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: 0.89 Conformation dependent library (CDL) restraints added in 41.7 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 52.6% alpha, 17.2% beta 139 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.617A pdb=" N LEU B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 6.304A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.13 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: 1410 1.33 - 1.45: 5254 1.45 - 1.57: 3498 1.57 - 1.69: 833 1.69 - 1.81: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 240 " pdb=" C4 A A 240 " ideal model delta sigma weight residual 1.374 1.391 -0.017 6.00e-03 2.78e+04 8.36e+00 bond pdb=" N9 G A 265 " pdb=" C4 G A 265 " ideal model delta sigma weight residual 1.375 1.393 -0.018 8.00e-03 1.56e+04 4.88e+00 bond pdb=" N9 G A 230 " pdb=" C4 G A 230 " ideal model delta sigma weight residual 1.375 1.391 -0.016 8.00e-03 1.56e+04 4.18e+00 bond pdb=" C2 C A 318 " pdb=" O2 C A 318 " ideal model delta sigma weight residual 1.240 1.226 0.014 9.00e-03 1.23e+04 2.35e+00 bond pdb=" C6 A A 257 " pdb=" N1 A A 257 " ideal model delta sigma weight residual 1.351 1.340 0.011 7.00e-03 2.04e+04 2.33e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 16673 1.92 - 3.84: 221 3.84 - 5.76: 40 5.76 - 7.68: 9 7.68 - 9.60: 1 Bond angle restraints: 16944 Sorted by residual: angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C6 C A 318 " ideal model delta sigma weight residual 120.80 127.76 -6.96 1.20e+00 6.94e-01 3.37e+01 angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sigma weight residual 118.80 113.05 5.75 1.10e+00 8.26e-01 2.73e+01 angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 118.36 3.54 7.00e-01 2.04e+00 2.56e+01 angle pdb=" C1' G A 265 " pdb=" N9 G A 265 " pdb=" C4 G A 265 " ideal model delta sigma weight residual 126.50 132.59 -6.09 1.30e+00 5.92e-01 2.19e+01 angle pdb=" C1' G A 379 " pdb=" N9 G A 379 " pdb=" C4 G A 379 " ideal model delta sigma weight residual 126.50 132.54 -6.04 1.30e+00 5.92e-01 2.16e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 5859 33.69 - 67.38: 1097 67.38 - 101.06: 150 101.06 - 134.75: 6 134.75 - 168.44: 4 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual -160.00 -51.19 -108.81 1 1.50e+01 4.44e-03 5.64e+01 dihedral pdb=" O4' C A 318 " pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sinusoidal sigma weight residual -160.00 -85.43 -74.57 1 1.50e+01 4.44e-03 3.13e+01 dihedral pdb=" O4' U A 34 " pdb=" C1' U A 34 " pdb=" N1 U A 34 " pdb=" C2 U A 34 " ideal model delta sinusoidal sigma weight residual -160.00 -86.34 -73.66 1 1.50e+01 4.44e-03 3.07e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2041 0.050 - 0.101: 143 0.101 - 0.151: 28 0.151 - 0.201: 7 0.201 - 0.252: 2 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C1' G A 269 " pdb=" O4' G A 269 " pdb=" C2' G A 269 " pdb=" N9 G A 269 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P A A 205 " pdb=" OP1 A A 205 " pdb=" OP2 A A 205 " pdb=" O5' A A 205 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1' A A 356 " pdb=" O4' A A 356 " pdb=" C2' A A 356 " pdb=" N9 A A 356 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.037 2.00e-02 2.50e+03 1.59e-02 7.61e+00 pdb=" N9 G A 298 " -0.039 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 298 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 262 " -0.032 2.00e-02 2.50e+03 1.61e-02 7.13e+00 pdb=" N9 A A 262 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A A 262 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A 262 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 262 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 262 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A A 262 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A A 262 " 0.017 2.00e-02 2.50e+03 pdb=" C2 A A 262 " -0.011 2.00e-02 2.50e+03 pdb=" N3 A A 262 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A 262 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 269 " 0.032 2.00e-02 2.50e+03 1.44e-02 6.22e+00 pdb=" N9 G A 269 " -0.036 2.00e-02 2.50e+03 pdb=" C8 G A 269 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 269 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 269 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 269 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 269 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G A 269 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G A 269 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 269 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G A 269 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 269 " -0.001 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 29 2.53 - 3.13: 7116 3.13 - 3.72: 21773 3.72 - 4.31: 28464 4.31 - 4.90: 35651 Nonbonded interactions: 93033 Sorted by model distance: nonbonded pdb="MG MG A 505 " pdb=" O HOH A 601 " model vdw 1.943 2.170 nonbonded pdb=" OP1 A A 50 " pdb="MG MG A 505 " model vdw 1.962 2.170 nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 509 " model vdw 1.974 2.170 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 512 " model vdw 1.980 2.170 nonbonded pdb=" OP2 A A 82 " pdb="MG MG A 521 " model vdw 1.990 2.170 ... (remaining 93028 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 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: 6.570 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11000 Z= 0.254 Angle : 0.593 9.597 16944 Z= 0.551 Chirality : 0.031 0.252 2221 Planarity : 0.004 0.022 581 Dihedral : 25.971 168.437 6900 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 1.75 % Allowed : 4.39 % Favored : 93.86 % Rotamer: Outliers : 2.02 % Allowed : 30.30 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.79), residues: 114 helix: 1.17 (0.76), residues: 46 sheet: 0.22 (0.95), residues: 26 loop : -2.13 (0.96), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.007 0.001 TYR B 94 PHE 0.004 0.001 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.25 (11000) covalent geometry : angle 0.59326 / 0.55 (16944) hydrogen bonds : bond 0.10109 / 10.83 ( 408) hydrogen bonds : angle 2.99698 / 3.13 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.118 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0995 time to fit residues: 3.3564 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.070295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.040001 restraints weight = 56997.316| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.52 r_work: 0.2610 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 11000 Z= 0.486 Angle : 0.765 10.225 16944 Z= 0.445 Chirality : 0.050 0.321 2221 Planarity : 0.006 0.035 581 Dihedral : 26.243 168.304 6650 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 1.75 % Allowed : 6.14 % Favored : 92.11 % Rotamer: Outliers : 11.11 % Allowed : 21.21 % Favored : 67.68 % 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: -1.15 (0.73), residues: 114 helix: 0.73 (0.72), residues: 48 sheet: -1.51 (0.73), residues: 26 loop : -2.00 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.014 0.003 TYR B 63 PHE 0.015 0.004 PHE B 41 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.49 (11000) covalent geometry : angle 0.76455 / 0.45 (16944) hydrogen bonds : bond 0.11888 / 11.43 ( 408) hydrogen bonds : angle 2.81692 / 3.34 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.083 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 29 average time/residue: 0.0746 time to fit residues: 3.0776 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.071398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041632 restraints weight = 61235.620| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.87 r_work: 0.2628 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11000 Z= 0.334 Angle : 0.595 9.626 16944 Z= 0.361 Chirality : 0.040 0.297 2221 Planarity : 0.005 0.027 581 Dihedral : 26.386 167.848 6650 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 1.75 % Allowed : 6.14 % Favored : 92.11 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % Favored : 66.67 % 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: -1.12 (0.73), residues: 114 helix: 0.92 (0.72), residues: 48 sheet: -1.72 (0.72), residues: 26 loop : -2.05 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.009 0.002 TYR B 31 PHE 0.010 0.002 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.33 (11000) covalent geometry : angle 0.59489 / 0.36 (16944) hydrogen bonds : bond 0.08975 / 8.50 ( 408) hydrogen bonds : angle 2.52527 / 2.98 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.112 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 29 average time/residue: 0.0877 time to fit residues: 3.5498 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.071097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041417 restraints weight = 61261.330| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.72 r_work: 0.2627 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11000 Z= 0.308 Angle : 0.582 9.694 16944 Z= 0.353 Chirality : 0.040 0.291 2221 Planarity : 0.005 0.029 581 Dihedral : 26.381 166.534 6650 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 1.75 % Allowed : 5.26 % Favored : 92.98 % Rotamer: Outliers : 9.09 % Allowed : 23.23 % Favored : 67.68 % 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: -1.26 (0.73), residues: 114 helix: 0.79 (0.73), residues: 48 sheet: -1.91 (0.69), residues: 26 loop : -2.01 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 35 TYR 0.009 0.001 TYR B 31 PHE 0.011 0.002 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.31 (11000) covalent geometry : angle 0.58169 / 0.35 (16944) hydrogen bonds : bond 0.08953 / 8.45 ( 408) hydrogen bonds : angle 2.51496 / 3.00 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.095 Fit side-chains REVERT: B 37 GLU cc_start: 0.8618 (pm20) cc_final: 0.8392 (pm20) outliers start: 9 outliers final: 7 residues processed: 31 average time/residue: 0.0848 time to fit residues: 3.6958 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.069522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.039510 restraints weight = 57305.367| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.29 r_work: 0.2598 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11000 Z= 0.389 Angle : 0.657 9.879 16944 Z= 0.393 Chirality : 0.044 0.304 2221 Planarity : 0.006 0.030 581 Dihedral : 26.480 166.990 6650 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 1.75 % Allowed : 5.26 % Favored : 92.98 % Rotamer: Outliers : 12.12 % Allowed : 23.23 % Favored : 64.65 % 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: -1.19 (0.73), residues: 114 helix: 1.12 (0.74), residues: 48 sheet: -2.15 (0.66), residues: 26 loop : -2.13 (0.92), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.007 0.002 TYR B 31 PHE 0.019 0.003 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.39 (11000) covalent geometry : angle 0.65739 / 0.39 (16944) hydrogen bonds : bond 0.10436 / 10.03 ( 408) hydrogen bonds : angle 2.69168 / 3.22 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.102 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 32 average time/residue: 0.0740 time to fit residues: 3.4830 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.070460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.040667 restraints weight = 57146.932| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.33 r_work: 0.2644 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11000 Z= 0.209 Angle : 0.530 9.276 16944 Z= 0.327 Chirality : 0.037 0.280 2221 Planarity : 0.005 0.032 581 Dihedral : 26.436 167.515 6650 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 1.75 % Allowed : 6.14 % Favored : 92.11 % Rotamer: Outliers : 9.09 % Allowed : 25.25 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.77), residues: 114 helix: 1.32 (0.72), residues: 48 sheet: -2.10 (0.69), residues: 26 loop : -1.64 (1.08), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 57 TYR 0.011 0.001 TYR B 94 PHE 0.011 0.002 PHE B 17 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.21 (11000) covalent geometry : angle 0.53015 / 0.33 (16944) hydrogen bonds : bond 0.08056 / 7.61 ( 408) hydrogen bonds : angle 2.45321 / 2.89 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.085 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 31 average time/residue: 0.0670 time to fit residues: 3.1601 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.068602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038358 restraints weight = 57880.624| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.72 r_work: 0.2557 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 11000 Z= 0.548 Angle : 0.768 11.449 16944 Z= 0.452 Chirality : 0.052 0.312 2221 Planarity : 0.006 0.034 581 Dihedral : 26.550 167.488 6650 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 29.43 Ramachandran Plot: Outliers : 1.75 % Allowed : 7.89 % Favored : 90.35 % Rotamer: Outliers : 10.10 % Allowed : 27.27 % Favored : 62.63 % 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: -1.41 (0.73), residues: 114 helix: 0.88 (0.72), residues: 48 sheet: -2.49 (0.64), residues: 26 loop : -1.97 (0.97), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.006 0.002 TYR B 81 PHE 0.014 0.003 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.55 (11000) covalent geometry : angle 0.76830 / 0.45 (16944) hydrogen bonds : bond 0.12521 / 12.24 ( 408) hydrogen bonds : angle 2.86149 / 3.52 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.129 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 27 average time/residue: 0.0741 time to fit residues: 3.0038 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.068618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038635 restraints weight = 57661.493| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.75 r_work: 0.2568 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 11000 Z= 0.448 Angle : 0.700 10.089 16944 Z= 0.418 Chirality : 0.048 0.311 2221 Planarity : 0.006 0.040 581 Dihedral : 26.672 168.369 6650 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 26.91 Ramachandran Plot: Outliers : 1.75 % Allowed : 7.02 % Favored : 91.23 % Rotamer: Outliers : 10.10 % Allowed : 26.26 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.76), residues: 114 helix: 0.98 (0.76), residues: 48 sheet: -2.75 (0.63), residues: 26 loop : -2.01 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.008 0.002 TYR B 31 PHE 0.012 0.003 PHE B 17 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.45 (11000) covalent geometry : angle 0.70034 / 0.42 (16944) hydrogen bonds : bond 0.10814 / 10.72 ( 408) hydrogen bonds : angle 2.72688 / 3.31 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.094 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 29 average time/residue: 0.0766 time to fit residues: 3.2028 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 64.1771 > 50: distance: 10 - 29: 3.029 distance: 33 - 94: 30.442 distance: 36 - 91: 22.810 distance: 45 - 75: 29.273 distance: 48 - 72: 25.447 distance: 60 - 65: 29.174 distance: 65 - 66: 38.467 distance: 65 - 224: 25.960 distance: 66 - 67: 47.973 distance: 66 - 69: 15.862 distance: 67 - 68: 49.787 distance: 67 - 72: 25.993 distance: 68 - 221: 26.773 distance: 69 - 70: 28.405 distance: 69 - 71: 42.884 distance: 72 - 73: 55.728 distance: 73 - 74: 59.256 distance: 73 - 76: 37.593 distance: 74 - 75: 22.484 distance: 74 - 79: 51.687 distance: 76 - 77: 38.568 distance: 76 - 78: 40.191 distance: 79 - 80: 42.690 distance: 79 - 210: 32.836 distance: 80 - 81: 31.842 distance: 81 - 82: 32.697 distance: 81 - 91: 35.896 distance: 82 - 207: 28.086 distance: 83 - 84: 3.006 distance: 84 - 85: 38.278 distance: 84 - 86: 18.293 distance: 85 - 87: 18.241 distance: 86 - 88: 28.184 distance: 87 - 89: 17.118 distance: 88 - 89: 23.918 distance: 89 - 90: 7.696 distance: 91 - 92: 4.924 distance: 92 - 93: 24.751 distance: 92 - 95: 23.324 distance: 93 - 94: 4.994 distance: 93 - 98: 35.398 distance: 95 - 96: 20.817 distance: 95 - 97: 10.999 distance: 98 - 99: 8.675 distance: 98 - 193: 26.230 distance: 99 - 100: 3.855 distance: 99 - 102: 11.068 distance: 100 - 101: 23.445 distance: 100 - 106: 38.995 distance: 101 - 190: 23.634 distance: 102 - 103: 31.844 distance: 103 - 104: 9.155 distance: 103 - 105: 19.877 distance: 106 - 107: 12.820 distance: 107 - 108: 7.286 distance: 107 - 110: 29.739 distance: 108 - 109: 18.776 distance: 108 - 114: 21.883 distance: 110 - 111: 17.455 distance: 111 - 112: 17.629 distance: 111 - 113: 11.040 distance: 114 - 115: 11.991 distance: 115 - 116: 31.446 distance: 115 - 118: 3.426 distance: 116 - 117: 25.526 distance: 116 - 125: 22.762 distance: 118 - 119: 14.932 distance: 119 - 120: 24.965 distance: 120 - 121: 31.590 distance: 121 - 122: 11.758 distance: 122 - 123: 10.748 distance: 125 - 126: 33.675 distance: 125 - 131: 50.600 distance: 126 - 127: 49.560 distance: 126 - 129: 39.453 distance: 127 - 128: 14.540 distance: 127 - 132: 15.151 distance: 129 - 130: 16.682 distance: 130 - 131: 38.791 distance: 132 - 133: 12.162 distance: 133 - 134: 48.681 distance: 133 - 136: 30.908 distance: 134 - 135: 15.571 distance: 134 - 141: 33.401 distance: 136 - 137: 26.427 distance: 137 - 138: 14.159 distance: 138 - 139: 34.441 distance: 138 - 140: 48.589 distance: 141 - 142: 22.706 distance: 142 - 145: 40.099 distance: 143 - 144: 4.149 distance: 143 - 150: 32.220 distance: 145 - 146: 4.748 distance: 146 - 147: 50.412 distance: 147 - 148: 13.133 distance: 147 - 149: 30.075