Starting phenix.real_space_refine on Thu Jun 4 02:31:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zi9_74266/06_2026/9zi9_74266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zi9_74266/06_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_74266/06_2026/9zi9_74266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zi9_74266/06_2026/9zi9_74266.map" model { file = "/net/cci-nas-00/data/ceres_data/9zi9_74266/06_2026/9zi9_74266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zi9_74266/06_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-dev-6079/lib/python3.9/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: 2.70, per 1000 atoms: 0.27 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: 0.74 Conformation dependent library (CDL) restraints added in 63.9 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: 2.08 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: 2.31 Time building geometry restraints manager: 1.02 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=" C3' U A 371 " pdb=" O3' U A 371 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.79e+00 bond pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta sigma weight residual 1.457 1.442 0.015 1.35e-02 5.49e+03 1.32e+00 bond pdb=" C3' U A 126 " pdb=" O3' U A 126 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.27e+00 bond pdb=" CB LYS B 113 " pdb=" CG LYS B 113 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C3' G A 204 " pdb=" O3' G A 204 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.24e+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=" C3' G A 204 " pdb=" O3' G A 204 " pdb=" P A A 205 " ideal model delta sigma weight residual 120.20 125.82 -5.62 1.50e+00 4.44e-01 1.40e+01 angle pdb=" C3' U A 371 " pdb=" O3' U A 371 " pdb=" P G A 372 " ideal model delta sigma weight residual 120.20 125.62 -5.42 1.50e+00 4.44e-01 1.31e+01 angle pdb=" C PHE B 17 " pdb=" N GLN B 18 " pdb=" CA GLN B 18 " ideal model delta sigma weight residual 122.37 117.21 5.16 1.54e+00 4.22e-01 1.12e+01 angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 114.04 109.95 4.09 1.24e+00 6.50e-01 1.09e+01 angle pdb=" O3' G A 204 " pdb=" P A A 205 " pdb=" OP2 A A 205 " ideal model delta sigma weight residual 108.00 117.60 -9.60 3.00e+00 1.11e-01 1.02e+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: 7.350 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.310 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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= 0.141 Angle : 0.593 9.597 16944 Z= 0.300 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 0.00258 / 0.14 (11000) covalent geometry : angle 0.59302 / 0.30 (16944) hydrogen bonds : bond 0.10109 / 5.84 ( 408) hydrogen bonds : angle 2.99698 / 2.20 ( 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 : 0.147 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0989 time to fit residues: 3.4016 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 : 0.140 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.070226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.040188 restraints weight = 57014.918| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.60 r_work: 0.2627 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11000 Z= 0.387 Angle : 0.752 9.694 16944 Z= 0.371 Chirality : 0.039 0.296 2221 Planarity : 0.005 0.025 581 Dihedral : 26.352 167.137 6650 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 1.75 % Allowed : 5.26 % Favored : 92.98 % Rotamer: Outliers : 8.08 % Allowed : 21.21 % Favored : 70.71 % 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: -0.86 (0.74), residues: 114 helix: 0.85 (0.70), residues: 48 sheet: -0.93 (0.79), residues: 26 loop : -2.02 (1.00), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 26 TYR 0.011 0.002 TYR B 5 PHE 0.005 0.002 PHE B 17 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.39 (11000) covalent geometry : angle 0.75187 / 0.37 (16944) hydrogen bonds : bond 0.08053 / 4.81 ( 408) hydrogen bonds : angle 2.46085 / 1.62 ( 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.150 Fit side-chains REVERT: B 14 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8956 (mm-40) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.1162 time to fit residues: 4.6003 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 96 GLU Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.071774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.042340 restraints weight = 61681.883| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.33 r_work: 0.2664 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11000 Z= 0.245 Angle : 0.632 9.791 16944 Z= 0.314 Chirality : 0.034 0.262 2221 Planarity : 0.004 0.023 581 Dihedral : 26.145 166.141 6650 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 1.75 % Allowed : 4.39 % Favored : 93.86 % Rotamer: Outliers : 6.06 % Allowed : 21.21 % Favored : 72.73 % 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: -0.89 (0.73), residues: 114 helix: 1.00 (0.71), residues: 48 sheet: -1.04 (0.78), residues: 26 loop : -2.22 (0.95), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.007 0.001 TYR B 31 PHE 0.007 0.002 PHE B 28 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.25 (11000) covalent geometry : angle 0.63183 / 0.31 (16944) hydrogen bonds : bond 0.06305 / 3.82 ( 408) hydrogen bonds : angle 2.28332 / 1.54 ( 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.089 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.1077 time to fit residues: 4.4223 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.071878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.042487 restraints weight = 61707.222| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.29 r_work: 0.2671 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11000 Z= 0.217 Angle : 0.625 9.776 16944 Z= 0.310 Chirality : 0.033 0.260 2221 Planarity : 0.004 0.023 581 Dihedral : 26.117 166.355 6650 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 1.75 % Allowed : 3.51 % Favored : 94.74 % 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: -0.89 (0.73), residues: 114 helix: 0.94 (0.70), residues: 48 sheet: -1.23 (0.75), residues: 26 loop : -1.98 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.010 0.001 TYR B 94 PHE 0.006 0.001 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.22 (11000) covalent geometry : angle 0.62498 / 0.31 (16944) hydrogen bonds : bond 0.06212 / 3.76 ( 408) hydrogen bonds : angle 2.21313 / 1.49 ( 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 : 0.143 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 32 average time/residue: 0.0983 time to fit residues: 4.5936 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain B residue 96 GLU 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: 8.9990 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.069616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.039639 restraints weight = 57280.222| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.37 r_work: 0.2618 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11000 Z= 0.324 Angle : 0.706 9.938 16944 Z= 0.347 Chirality : 0.037 0.257 2221 Planarity : 0.005 0.027 581 Dihedral : 26.292 166.953 6650 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 1.75 % Allowed : 4.39 % Favored : 93.86 % Rotamer: Outliers : 7.07 % Allowed : 29.29 % 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: -0.92 (0.73), residues: 114 helix: 0.95 (0.70), residues: 48 sheet: -1.46 (0.75), residues: 26 loop : -1.88 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.011 0.002 TYR B 94 PHE 0.009 0.002 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.32 (11000) covalent geometry : angle 0.70551 / 0.35 (16944) hydrogen bonds : bond 0.07394 / 4.43 ( 408) hydrogen bonds : angle 2.32730 / 1.50 ( 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.145 Fit side-chains REVERT: B 87 GLN cc_start: 0.9159 (tp40) cc_final: 0.8884 (tp-100) outliers start: 7 outliers final: 7 residues processed: 29 average time/residue: 0.0954 time to fit residues: 3.9980 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 : 0.129 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.072433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.043209 restraints weight = 61521.095| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.22 r_work: 0.2708 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11000 Z= 0.152 Angle : 0.596 9.904 16944 Z= 0.295 Chirality : 0.031 0.237 2221 Planarity : 0.004 0.023 581 Dihedral : 25.989 166.442 6650 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 1.75 % Allowed : 3.51 % Favored : 94.74 % Rotamer: Outliers : 7.07 % Allowed : 29.29 % 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: -0.69 (0.76), residues: 114 helix: 1.01 (0.70), residues: 48 sheet: -1.25 (0.73), residues: 26 loop : -1.63 (1.09), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.007 0.001 TYR B 31 PHE 0.007 0.001 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (11000) covalent geometry : angle 0.59607 / 0.30 (16944) hydrogen bonds : bond 0.05823 / 3.51 ( 408) hydrogen bonds : angle 2.18277 / 1.44 ( 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.152 Fit side-chains REVERT: B 18 GLN cc_start: 0.8538 (pp30) cc_final: 0.8022 (pp30) REVERT: B 42 ARG cc_start: 0.8692 (mtm180) cc_final: 0.8305 (mtm-85) outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.1336 time to fit residues: 5.4115 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 49 LYS Chi-restraints excluded: chain B residue 96 GLU 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: 10.0000 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.068865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039020 restraints weight = 56810.003| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.90 r_work: 0.2587 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 11000 Z= 0.409 Angle : 0.776 10.797 16944 Z= 0.380 Chirality : 0.039 0.257 2221 Planarity : 0.005 0.028 581 Dihedral : 26.349 167.290 6650 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 1.75 % Allowed : 4.39 % Favored : 93.86 % 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: -0.70 (0.79), residues: 114 helix: 1.08 (0.71), residues: 48 sheet: -1.70 (0.73), residues: 26 loop : -1.38 (1.16), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 57 TYR 0.012 0.002 TYR B 94 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 0.00770 / 0.41 (11000) covalent geometry : angle 0.77579 / 0.38 (16944) hydrogen bonds : bond 0.08359 / 4.97 ( 408) hydrogen bonds : angle 2.41159 / 1.53 ( 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.157 Fit side-chains REVERT: B 18 GLN cc_start: 0.8514 (pp30) cc_final: 0.8011 (pp30) REVERT: B 37 GLU cc_start: 0.8668 (pm20) cc_final: 0.8450 (pm20) outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 0.1025 time to fit residues: 4.2718 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 96 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.068938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039092 restraints weight = 56969.080| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.57 r_work: 0.2609 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 11000 Z= 0.358 Angle : 0.715 10.206 16944 Z= 0.352 Chirality : 0.038 0.255 2221 Planarity : 0.005 0.028 581 Dihedral : 26.334 167.357 6650 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.02 % Favored : 92.11 % Rotamer: Outliers : 10.10 % Allowed : 29.29 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.73), residues: 114 helix: 0.51 (0.70), residues: 48 sheet: -1.68 (0.73), residues: 26 loop : -1.70 (1.02), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 57 TYR 0.008 0.002 TYR B 94 PHE 0.011 0.003 PHE B 41 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.36 (11000) covalent geometry : angle 0.71533 / 0.35 (16944) hydrogen bonds : bond 0.07415 / 4.47 ( 408) hydrogen bonds : angle 2.42716 / 1.47 ( 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.138 Fit side-chains REVERT: B 18 GLN cc_start: 0.8547 (pp30) cc_final: 0.8051 (pp30) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.0930 time to fit residues: 4.3595 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 51 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.070929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043393 restraints weight = 60758.440| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.47 r_work: 0.2647 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11000 Z= 0.207 Angle : 0.647 10.160 16944 Z= 0.320 Chirality : 0.033 0.246 2221 Planarity : 0.004 0.028 581 Dihedral : 26.215 167.869 6648 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.02 % Favored : 92.11 % 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: -0.72 (0.76), residues: 114 helix: 1.16 (0.71), residues: 48 sheet: -1.65 (0.75), residues: 26 loop : -1.59 (1.04), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 57 TYR 0.009 0.001 TYR B 94 PHE 0.006 0.001 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.21 (11000) covalent geometry : angle 0.64661 / 0.32 (16944) hydrogen bonds : bond 0.06434 / 3.88 ( 408) hydrogen bonds : angle 2.36987 / 1.46 ( 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.147 Fit side-chains REVERT: B 18 GLN cc_start: 0.8493 (pp30) cc_final: 0.8056 (pp30) outliers start: 6 outliers final: 6 residues processed: 30 average time/residue: 0.1032 time to fit residues: 4.4734 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 51 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.068681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038805 restraints weight = 56401.514| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.58 r_work: 0.2592 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 11000 Z= 0.368 Angle : 0.739 10.241 16944 Z= 0.364 Chirality : 0.038 0.257 2221 Planarity : 0.005 0.029 581 Dihedral : 26.376 168.204 6648 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % 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: -0.82 (0.75), residues: 114 helix: 1.17 (0.72), residues: 48 sheet: -1.79 (0.74), residues: 26 loop : -1.71 (0.99), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 57 TYR 0.011 0.002 TYR B 94 PHE 0.009 0.002 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.37 (11000) covalent geometry : angle 0.73883 / 0.36 (16944) hydrogen bonds : bond 0.07881 / 4.72 ( 408) hydrogen bonds : angle 2.53453 / 1.53 ( 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.146 Fit side-chains REVERT: B 18 GLN cc_start: 0.8477 (pp30) cc_final: 0.8023 (pp30) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.1027 time to fit residues: 4.3895 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.071066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.041727 restraints weight = 57427.748| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.24 r_work: 0.2712 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11000 Z= 0.150 Angle : 0.615 10.176 16944 Z= 0.303 Chirality : 0.031 0.234 2221 Planarity : 0.004 0.021 581 Dihedral : 26.045 167.901 6648 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.05 % Allowed : 32.32 % 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: -0.61 (0.76), residues: 114 helix: 1.18 (0.70), residues: 48 sheet: -1.55 (0.78), residues: 26 loop : -1.46 (1.05), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 57 TYR 0.006 0.001 TYR B 5 PHE 0.007 0.001 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (11000) covalent geometry : angle 0.61450 / 0.30 (16944) hydrogen bonds : bond 0.06052 / 3.65 ( 408) hydrogen bonds : angle 2.28280 / 1.39 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.21 seconds wall clock time: 65 minutes 24.54 seconds (3924.54 seconds total)