Starting phenix.real_space_refine on Wed Aug 5 13:09:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zi9_74266/08_2026/9zi9_74266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zi9_74266/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9zi9_74266/08_2026/9zi9_74266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zi9_74266/08_2026/9zi9_74266.map" model { file = "/net/cci-nas-00/data/ceres_data/9zi9_74266/08_2026/9zi9_74266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zi9_74266/08_2026/9zi9_74266.cif" } 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-2.2rc3-6140/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: 2.59, per 1000 atoms: 0.26 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: 0.95 Conformation dependent library (CDL) restraints added in 85.2 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: 1.86 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: 2.38 Time building geometry restraints manager: 1.27 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=" C3' U A 371 " pdb=" O3' U A 371 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.20e-02 6.94e+03 2.79e+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 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15659 1.92 - 3.84: 1231 3.84 - 5.76: 42 5.76 - 7.68: 11 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=" C3' G A 204 " pdb=" O3' G A 204 " pdb=" P A A 205 " ideal model delta sigma weight residual 119.70 125.82 -6.12 1.20e+00 6.94e-01 2.60e+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=" C3' U A 371 " pdb=" O3' U A 371 " pdb=" P G A 372 " ideal model delta sigma weight residual 119.70 125.62 -5.92 1.20e+00 6.94e-01 2.43e+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 - 0.053: 1612 0.053 - 0.106: 195 0.106 - 0.159: 404 0.159 - 0.212: 8 0.212 - 0.265: 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 2.47 2.21 0.26 2.00e-01 2.50e+01 1.75e+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=" C2' C A 318 " pdb=" C3' C A 318 " pdb=" O2' C A 318 " pdb=" C1' C A 318 " both_signs ideal model delta sigma weight residual False -2.62 -2.82 0.20 2.00e-01 2.50e+01 1.04e+00 ... (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: 9.840 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: 0.300 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- 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= 0.286 Angle : 0.864 9.597 16944 Z= 0.736 Chirality : 0.064 0.265 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 0.00298 / 0.29 (11000) covalent geometry : angle 0.86420 / 0.74 (16944) hydrogen bonds : bond 0.10109 / 11.35 ( 408) hydrogen bonds : angle 2.99698 / 3.47 ( 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 : 0.145 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1093 time to fit residues: 3.7773 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 : 0.147 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.070190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.039936 restraints weight = 57339.853| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.02 r_work: 0.2600 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 11000 Z= 0.521 Angle : 0.975 10.953 16944 Z= 0.493 Chirality : 0.069 0.319 2221 Planarity : 0.007 0.041 581 Dihedral : 26.193 171.362 6650 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 30.27 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: -1.17 (0.74), residues: 114 helix: 0.65 (0.72), residues: 48 sheet: -1.52 (0.73), residues: 26 loop : -1.92 (1.00), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.015 0.003 TYR B 5 PHE 0.013 0.004 PHE B 41 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.52 (11000) covalent geometry : angle 0.97455 / 0.49 (16944) hydrogen bonds : bond 0.12330 / 12.86 ( 408) hydrogen bonds : angle 2.91850 / 3.72 ( 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.144 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 26 average time/residue: 0.1211 time to fit residues: 4.3899 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE 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: 7.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 overall best weight: 5.3186 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.070256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039962 restraints weight = 58040.664| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.44 r_work: 0.2612 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11000 Z= 0.364 Angle : 0.780 10.082 16944 Z= 0.411 Chirality : 0.055 0.316 2221 Planarity : 0.006 0.031 581 Dihedral : 26.376 170.793 6650 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 1.75 % Allowed : 6.14 % Favored : 92.11 % Rotamer: Outliers : 11.11 % Allowed : 20.20 % Favored : 68.69 % 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: -1.34 (0.73), residues: 114 helix: 0.77 (0.73), residues: 48 sheet: -1.96 (0.70), residues: 26 loop : -2.09 (0.95), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.012 0.002 TYR B 31 PHE 0.009 0.002 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.36 (11000) covalent geometry : angle 0.77961 / 0.41 (16944) hydrogen bonds : bond 0.10081 / 10.52 ( 408) hydrogen bonds : angle 2.65930 / 3.40 ( 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.129 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 30 average time/residue: 0.1016 time to fit residues: 4.2208 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 overall best weight: 4.1384 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.070107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040111 restraints weight = 57622.879| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.34 r_work: 0.2621 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11000 Z= 0.310 Angle : 0.705 10.005 16944 Z= 0.381 Chirality : 0.048 0.312 2221 Planarity : 0.005 0.029 581 Dihedral : 26.379 168.755 6650 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 1.75 % Allowed : 5.26 % Favored : 92.98 % 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: -1.30 (0.74), residues: 114 helix: 0.79 (0.73), residues: 48 sheet: -2.16 (0.69), residues: 26 loop : -1.88 (0.99), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.010 0.002 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 0.00498 / 0.31 (11000) covalent geometry : angle 0.70466 / 0.38 (16944) hydrogen bonds : bond 0.09673 / 10.07 ( 408) hydrogen bonds : angle 2.59190 / 3.32 ( 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.105 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.0714 time to fit residues: 3.1328 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 49 LYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.069344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.039741 restraints weight = 60768.323| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.84 r_work: 0.2555 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 11000 Z= 0.493 Angle : 0.959 11.101 16944 Z= 0.488 Chirality : 0.065 0.330 2221 Planarity : 0.007 0.034 581 Dihedral : 26.586 170.005 6650 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 32.28 Ramachandran Plot: Outliers : 1.75 % Allowed : 7.89 % Favored : 90.35 % Rotamer: Outliers : 14.14 % Allowed : 21.21 % 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: -1.67 (0.73), residues: 114 helix: 0.71 (0.75), residues: 48 sheet: -2.67 (0.60), residues: 26 loop : -2.14 (0.91), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.008 0.002 TYR B 94 PHE 0.016 0.004 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.49 (11000) covalent geometry : angle 0.95913 / 0.49 (16944) hydrogen bonds : bond 0.13397 / 14.10 ( 408) hydrogen bonds : angle 3.01508 / 3.87 ( 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.132 Fit side-chains REVERT: B 26 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8528 (ptp90) outliers start: 14 outliers final: 7 residues processed: 30 average time/residue: 0.0792 time to fit residues: 3.5725 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 36 optimal weight: 50.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.070669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041151 restraints weight = 60976.348| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.30 r_work: 0.2614 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11000 Z= 0.218 Angle : 0.636 9.546 16944 Z= 0.361 Chirality : 0.043 0.314 2221 Planarity : 0.005 0.033 581 Dihedral : 26.450 171.199 6650 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 1.75 % Allowed : 7.89 % Favored : 90.35 % Rotamer: Outliers : 8.08 % Allowed : 28.28 % 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: -1.08 (0.76), residues: 114 helix: 1.10 (0.73), residues: 48 sheet: -2.33 (0.68), residues: 26 loop : -1.74 (1.02), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.009 0.001 TYR B 31 PHE 0.014 0.002 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.22 (11000) covalent geometry : angle 0.63609 / 0.36 (16944) hydrogen bonds : bond 0.09201 / 9.75 ( 408) hydrogen bonds : angle 2.57760 / 3.29 ( 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.184 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 28 average time/residue: 0.0921 time to fit residues: 3.7174 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 overall best weight: 8.1792 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.068249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038234 restraints weight = 58165.316| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.27 r_work: 0.2544 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 11000 Z= 0.566 Angle : 1.035 11.570 16944 Z= 0.512 Chirality : 0.070 0.329 2221 Planarity : 0.007 0.037 581 Dihedral : 26.550 170.276 6650 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 1.75 % Allowed : 7.89 % Favored : 90.35 % Rotamer: Outliers : 9.09 % Allowed : 29.29 % Favored : 61.62 % 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: -1.86 (0.72), residues: 114 helix: 0.54 (0.73), residues: 48 sheet: -2.83 (0.61), residues: 26 loop : -2.17 (0.91), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.008 0.002 TYR B 94 PHE 0.013 0.003 PHE B 41 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.57 (11000) covalent geometry : angle 1.03476 / 0.51 (16944) hydrogen bonds : bond 0.13455 / 14.23 ( 408) hydrogen bonds : angle 2.99607 / 3.90 ( 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.223 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 25 average time/residue: 0.0933 time to fit residues: 3.4837 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 7 ILE 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 101 LEU Chi-restraints excluded: chain B residue 102 ILE 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: 0.9980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 40.0000 overall best weight: 7.7988 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.068023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038347 restraints weight = 58717.805| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 1.94 r_work: 0.2551 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 11000 Z= 0.520 Angle : 1.021 12.077 16944 Z= 0.515 Chirality : 0.068 0.317 2221 Planarity : 0.007 0.043 581 Dihedral : 26.812 172.747 6650 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 34.35 Ramachandran Plot: Outliers : 1.75 % Allowed : 8.77 % Favored : 89.47 % Rotamer: Outliers : 10.10 % Allowed : 30.30 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.71), residues: 114 helix: 0.41 (0.72), residues: 48 sheet: -2.99 (0.62), residues: 26 loop : -2.59 (0.87), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B 35 TYR 0.009 0.002 TYR B 5 PHE 0.018 0.004 PHE B 17 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.52 (11000) covalent geometry : angle 1.02147 / 0.51 (16944) hydrogen bonds : bond 0.13154 / 14.26 ( 408) hydrogen bonds : angle 3.03526 / 3.86 ( 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.154 Fit side-chains REVERT: B 19 GLN cc_start: 0.8881 (mp10) cc_final: 0.8599 (mp10) REVERT: B 37 GLU cc_start: 0.8715 (pm20) cc_final: 0.8404 (pm20) outliers start: 10 outliers final: 9 residues processed: 29 average time/residue: 0.0798 time to fit residues: 3.2874 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR 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 82 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 30.0000 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 40.0000 chunk 6 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.070146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.040703 restraints weight = 57358.581| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.21 r_work: 0.2677 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11000 Z= 0.150 Angle : 0.612 10.693 16944 Z= 0.355 Chirality : 0.040 0.315 2221 Planarity : 0.005 0.035 581 Dihedral : 26.527 173.888 6650 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 1.75 % Allowed : 7.89 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 32.32 % Favored : 61.62 % 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: -1.24 (0.77), residues: 114 helix: 0.91 (0.71), residues: 48 sheet: -2.36 (0.71), residues: 26 loop : -1.76 (1.10), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B 6 TYR 0.010 0.002 TYR B 31 PHE 0.012 0.002 PHE B 17 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.15 (11000) covalent geometry : angle 0.61173 / 0.35 (16944) hydrogen bonds : bond 0.09203 / 9.88 ( 408) hydrogen bonds : angle 2.57930 / 3.28 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.124 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 32 average time/residue: 0.0896 time to fit residues: 4.0919 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.067629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037994 restraints weight = 57867.176| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.39 r_work: 0.2545 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 11000 Z= 0.626 Angle : 1.121 12.161 16944 Z= 0.542 Chirality : 0.076 0.377 2221 Planarity : 0.007 0.042 581 Dihedral : 26.523 171.747 6650 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 34.61 Ramachandran Plot: Outliers : 0.88 % Allowed : 13.16 % Favored : 85.96 % Rotamer: Outliers : 9.09 % Allowed : 32.32 % Favored : 58.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.71), residues: 114 helix: -0.01 (0.70), residues: 48 sheet: -2.88 (0.63), residues: 26 loop : -2.30 (0.95), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 65 TYR 0.011 0.003 TYR B 5 PHE 0.019 0.005 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00982 / 0.63 (11000) covalent geometry : angle 1.12139 / 0.54 (16944) hydrogen bonds : bond 0.13611 / 14.36 ( 408) hydrogen bonds : angle 3.22544 / 4.29 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.146 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 27 average time/residue: 0.1028 time to fit residues: 3.9974 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.069718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.040126 restraints weight = 57718.180| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.23 r_work: 0.2647 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11000 Z= 0.154 Angle : 0.617 10.200 16944 Z= 0.355 Chirality : 0.041 0.315 2221 Planarity : 0.005 0.038 581 Dihedral : 26.494 174.460 6650 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.65 % Favored : 89.47 % Rotamer: Outliers : 7.07 % Allowed : 33.33 % Favored : 59.60 % 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: -1.47 (0.76), residues: 114 helix: 0.61 (0.72), residues: 48 sheet: -2.41 (0.69), residues: 26 loop : -1.77 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B 65 TYR 0.011 0.002 TYR B 94 PHE 0.013 0.002 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (11000) covalent geometry : angle 0.61728 / 0.36 (16944) hydrogen bonds : bond 0.09174 / 9.81 ( 408) hydrogen bonds : angle 2.77014 / 3.64 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3191.32 seconds wall clock time: 55 minutes 11.62 seconds (3311.62 seconds total)