Starting phenix.real_space_refine on Thu Jul 2 19:51:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zic_74269/07_2026/9zic_74269.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zic_74269/07_2026/9zic_74269.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/9zic_74269/07_2026/9zic_74269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zic_74269/07_2026/9zic_74269.map" model { file = "/net/cci-nas-00/data/ceres_data/9zic_74269/07_2026/9zic_74269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zic_74269/07_2026/9zic_74269.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 24 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9933 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': 25, 'rna2p_pyr': 15, 'rna3p_pur': 218, 'rna3p_pyr': 159} Link IDs: {'rna2p': 40, 'rna3p': 376} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Unusual residues: {' MG': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Time building chain proxies: 1.32, per 1000 atoms: 0.13 Number of scatterers: 9933 At special positions: 0 Unit cell: (125.172, 166.896, 147.864, 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 24 11.99 O 3051 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: 0.69 Conformation dependent library (CDL) restraints added in 40.7 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 44.0% alpha, 17.2% beta 139 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'B' and resid 9 through 19 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 109 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.511A pdb=" N VAL B 21 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 0.90 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: 1093 1.33 - 1.45: 5296 1.45 - 1.57: 3773 1.57 - 1.69: 833 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N7 A A 332 " pdb=" C5 A A 332 " ideal model delta sigma weight residual 1.388 1.377 0.011 6.00e-03 2.78e+04 3.10e+00 bond pdb=" N7 A A 48 " pdb=" C5 A A 48 " ideal model delta sigma weight residual 1.388 1.379 0.009 6.00e-03 2.78e+04 2.24e+00 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.365 0.009 6.00e-03 2.78e+04 2.23e+00 bond pdb=" N9 A A 350 " pdb=" C4 A A 350 " ideal model delta sigma weight residual 1.374 1.383 -0.009 6.00e-03 2.78e+04 2.21e+00 bond pdb=" C8 A A 332 " pdb=" N7 A A 332 " ideal model delta sigma weight residual 1.311 1.301 0.010 7.00e-03 2.04e+04 2.07e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 16932 5.40 - 10.79: 9 10.79 - 16.19: 1 16.19 - 21.58: 0 21.58 - 26.98: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O3' G A 114 " pdb=" P C A 115 " pdb=" OP1 C A 115 " ideal model delta sigma weight residual 108.00 81.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" O3' G A 114 " pdb=" P C A 115 " pdb=" OP2 C A 115 " ideal model delta sigma weight residual 108.00 83.36 24.64 3.00e+00 1.11e-01 6.74e+01 angle pdb=" O4 U A 199 " pdb=" C4 U A 199 " pdb=" C5 U A 199 " ideal model delta sigma weight residual 125.90 129.54 -3.64 6.00e-01 2.78e+00 3.68e+01 angle pdb=" N3 U A 199 " pdb=" C4 U A 199 " pdb=" O4 U A 199 " ideal model delta sigma weight residual 119.40 115.78 3.62 7.00e-01 2.04e+00 2.68e+01 angle pdb=" C2' A A 195 " pdb=" C1' A A 195 " pdb=" N9 A A 195 " ideal model delta sigma weight residual 112.00 118.94 -6.94 1.50e+00 4.44e-01 2.14e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 5986 35.85 - 71.70: 989 71.70 - 107.55: 133 107.55 - 143.40: 3 143.40 - 179.25: 5 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 200.00 30.72 169.28 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 -42.67 -117.33 1 1.50e+01 4.44e-03 6.23e+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 -57.51 -102.49 1 1.50e+01 4.44e-03 5.19e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.387: 2220 0.387 - 0.774: 0 0.774 - 1.161: 0 1.161 - 1.548: 0 1.548 - 1.935: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P C A 115 " pdb=" OP1 C A 115 " pdb=" OP2 C A 115 " pdb=" O5' C A 115 " both_signs ideal model delta sigma weight residual True 2.41 0.47 1.94 2.00e-01 2.50e+01 9.37e+01 chirality pdb=" C1' A A 195 " pdb=" O4' A A 195 " pdb=" C2' A A 195 " pdb=" N9 A A 195 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' A A 146 " pdb=" C4' A A 146 " pdb=" O3' A A 146 " pdb=" C2' A A 146 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 195 " -0.070 2.00e-02 2.50e+03 3.19e-02 2.80e+01 pdb=" N9 A A 195 " 0.075 2.00e-02 2.50e+03 pdb=" C8 A A 195 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 195 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 195 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 195 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A A 195 " -0.019 2.00e-02 2.50e+03 pdb=" N1 A A 195 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A 195 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A A 195 " 0.013 2.00e-02 2.50e+03 pdb=" C4 A A 195 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.034 2.00e-02 2.50e+03 1.50e-02 6.72e+00 pdb=" N9 G A 298 " -0.037 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.003 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 232 " 0.024 2.00e-02 2.50e+03 1.54e-02 6.54e+00 pdb=" N9 A A 232 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A A 232 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A A 232 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A A 232 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A 232 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A A 232 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A A 232 " -0.020 2.00e-02 2.50e+03 pdb=" C2 A A 232 " 0.015 2.00e-02 2.50e+03 pdb=" N3 A A 232 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A A 232 " -0.001 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 44 2.54 - 3.13: 7098 3.13 - 3.72: 20971 3.72 - 4.31: 27681 4.31 - 4.90: 34789 Nonbonded interactions: 90583 Sorted by model distance: nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 508 " model vdw 1.953 2.170 nonbonded pdb=" OP2 A A 82 " pdb="MG MG A 518 " model vdw 1.987 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 509 " model vdw 2.001 2.170 nonbonded pdb=" OP2 G A 288 " pdb="MG MG A 517 " model vdw 2.002 2.170 nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 506 " model vdw 2.006 2.170 ... (remaining 90578 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: 9.050 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 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= 0.251 Angle : 0.633 26.976 16944 Z= 0.508 Chirality : 0.051 1.935 2221 Planarity : 0.004 0.032 581 Dihedral : 25.627 179.247 6900 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 35.35 % 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: 0.80 (0.85), residues: 114 helix: 2.31 (0.80), residues: 46 sheet: 0.84 (1.05), residues: 26 loop : -1.83 (1.00), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.009 0.002 TYR B 31 PHE 0.008 0.001 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.25 (11000) covalent geometry : angle 0.63312 / 0.51 (16944) hydrogen bonds : bond 0.10413 / 10.41 ( 400) hydrogen bonds : angle 3.77819 / 3.92 ( 749) *********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.137 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0733 time to fit residues: 2.0073 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.085993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.046998 restraints weight = 59932.105| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.31 r_work: 0.2680 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 11000 Z= 0.459 Angle : 0.729 27.190 16944 Z= 0.411 Chirality : 0.061 1.879 2221 Planarity : 0.006 0.029 581 Dihedral : 25.867 179.152 6645 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.04 % Allowed : 31.31 % 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: 0.16 (0.80), residues: 114 helix: 1.28 (0.68), residues: 48 sheet: 0.54 (1.03), residues: 26 loop : -1.66 (1.09), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.009 0.002 TYR B 31 PHE 0.021 0.005 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.46 (11000) covalent geometry : angle 0.72851 / 0.41 (16944) hydrogen bonds : bond 0.10677 / 10.58 ( 400) hydrogen bonds : angle 2.83961 / 3.13 ( 749) *********************** 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 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.090 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 0.0851 time to fit residues: 2.1285 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR 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 41 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.085874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050474 restraints weight = 60007.811| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.17 r_work: 0.2664 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11000 Z= 0.329 Angle : 0.644 26.971 16944 Z= 0.362 Chirality : 0.056 1.894 2221 Planarity : 0.005 0.020 581 Dihedral : 26.023 178.556 6645 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.04 % Allowed : 28.28 % 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: 0.42 (0.83), residues: 114 helix: 1.82 (0.71), residues: 48 sheet: 0.37 (1.07), residues: 26 loop : -1.77 (1.10), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.015 0.002 TYR B 40 PHE 0.019 0.002 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.33 (11000) covalent geometry : angle 0.64373 / 0.36 (16944) hydrogen bonds : bond 0.09308 / 9.33 ( 400) hydrogen bonds : angle 2.68451 / 2.99 ( 749) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.133 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 15 average time/residue: 0.0511 time to fit residues: 1.2828 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 40.0000 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 22 optimal weight: 50.0000 chunk 36 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 overall best weight: 6.1390 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.084383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045620 restraints weight = 60119.125| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.64 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 11000 Z= 0.491 Angle : 0.786 27.414 16944 Z= 0.443 Chirality : 0.062 1.867 2221 Planarity : 0.006 0.028 581 Dihedral : 26.208 178.883 6645 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.06 % Allowed : 30.30 % 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: -0.38 (0.82), residues: 114 helix: 0.64 (0.69), residues: 53 sheet: -0.29 (0.98), residues: 26 loop : -1.47 (1.27), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 86 TYR 0.019 0.003 TYR B 40 PHE 0.018 0.003 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.49 (11000) covalent geometry : angle 0.78595 / 0.44 (16944) hydrogen bonds : bond 0.13277 / 13.43 ( 400) hydrogen bonds : angle 3.09798 / 3.61 ( 749) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.141 Fit side-chains REVERT: B 92 MET cc_start: 0.8489 (ttt) cc_final: 0.8282 (ttt) outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 0.0702 time to fit residues: 1.7513 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.085544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048366 restraints weight = 60236.289| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.28 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11000 Z= 0.234 Angle : 0.608 26.965 16944 Z= 0.344 Chirality : 0.055 1.920 2221 Planarity : 0.004 0.023 581 Dihedral : 26.175 178.103 6645 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 30.30 % 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: 0.45 (0.84), residues: 114 helix: 1.89 (0.74), residues: 48 sheet: 0.27 (1.07), residues: 26 loop : -1.72 (1.10), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 57 TYR 0.012 0.002 TYR B 40 PHE 0.015 0.002 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.23 (11000) covalent geometry : angle 0.60756 / 0.34 (16944) hydrogen bonds : bond 0.08949 / 8.96 ( 400) hydrogen bonds : angle 2.69002 / 3.02 ( 749) *********************** 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 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.124 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 17 average time/residue: 0.0857 time to fit residues: 2.1819 Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 overall best weight: 5.5790 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.084460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045201 restraints weight = 60215.247| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.54 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 11000 Z= 0.435 Angle : 0.725 27.362 16944 Z= 0.409 Chirality : 0.060 1.875 2221 Planarity : 0.005 0.027 581 Dihedral : 26.198 178.329 6645 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 6.06 % Allowed : 30.30 % 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: -0.02 (0.84), residues: 114 helix: 0.99 (0.71), residues: 54 sheet: -0.06 (1.01), residues: 26 loop : -1.52 (1.29), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.017 0.002 TYR B 40 PHE 0.018 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.43 (11000) covalent geometry : angle 0.72512 / 0.41 (16944) hydrogen bonds : bond 0.11343 / 11.39 ( 400) hydrogen bonds : angle 2.93892 / 3.34 ( 749) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.141 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 0.0588 time to fit residues: 1.4590 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.084093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.044547 restraints weight = 59968.925| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.52 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 11000 Z= 0.427 Angle : 0.735 27.244 16944 Z= 0.414 Chirality : 0.061 1.879 2221 Planarity : 0.006 0.034 581 Dihedral : 26.343 178.150 6645 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 6.06 % Allowed : 31.31 % 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: 0.01 (0.84), residues: 114 helix: 1.12 (0.70), residues: 54 sheet: 0.23 (1.05), residues: 26 loop : -1.96 (1.25), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.023 0.004 TYR B 40 PHE 0.025 0.003 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.43 (11000) covalent geometry : angle 0.73478 / 0.41 (16944) hydrogen bonds : bond 0.10982 / 11.19 ( 400) hydrogen bonds : angle 2.99196 / 3.41 ( 749) *********************** 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 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.109 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 18 average time/residue: 0.0632 time to fit residues: 1.8493 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 36 optimal weight: 30.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.083015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044012 restraints weight = 59807.560| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.04 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.110 11000 Z= 0.643 Angle : 0.902 27.808 16944 Z= 0.505 Chirality : 0.068 1.829 2221 Planarity : 0.007 0.034 581 Dihedral : 26.505 178.584 6645 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 33.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % 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 (0.81), residues: 114 helix: 0.52 (0.69), residues: 54 sheet: -0.59 (0.93), residues: 26 loop : -2.12 (1.25), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 42 TYR 0.017 0.003 TYR B 40 PHE 0.016 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01104 / 0.64 (11000) covalent geometry : angle 0.90188 / 0.51 (16944) hydrogen bonds : bond 0.14841 / 15.25 ( 400) hydrogen bonds : angle 3.38507 / 3.87 ( 749) *********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.120 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 14 average time/residue: 0.0707 time to fit residues: 1.6401 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 15 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.084182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.045371 restraints weight = 60071.685| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.92 r_work: 0.2646 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11000 Z= 0.326 Angle : 0.688 27.369 16944 Z= 0.389 Chirality : 0.058 1.891 2221 Planarity : 0.005 0.026 581 Dihedral : 26.457 177.838 6645 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % 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: 0.04 (0.85), residues: 114 helix: 1.23 (0.72), residues: 54 sheet: -0.05 (1.01), residues: 26 loop : -1.84 (1.30), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.016 0.002 TYR B 40 PHE 0.010 0.002 PHE B 13 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.33 (11000) covalent geometry : angle 0.68755 / 0.39 (16944) hydrogen bonds : bond 0.09987 / 10.11 ( 400) hydrogen bonds : angle 2.95119 / 3.29 ( 749) *********************** 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 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.123 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 18 average time/residue: 0.0716 time to fit residues: 1.9322 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.083976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044855 restraints weight = 59254.274| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.18 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11000 Z= 0.370 Angle : 0.699 27.295 16944 Z= 0.394 Chirality : 0.059 1.888 2221 Planarity : 0.005 0.028 581 Dihedral : 26.387 177.091 6645 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 5.05 % Allowed : 34.34 % 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: 0.02 (0.85), residues: 114 helix: 1.26 (0.72), residues: 54 sheet: -0.15 (0.99), residues: 26 loop : -1.84 (1.31), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.014 0.002 TYR B 40 PHE 0.011 0.002 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.37 (11000) covalent geometry : angle 0.69881 / 0.39 (16944) hydrogen bonds : bond 0.10213 / 10.20 ( 400) hydrogen bonds : angle 2.97018 / 3.30 ( 749) ********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.139 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 16 average time/residue: 0.0599 time to fit residues: 1.6811 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 12 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.084620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045763 restraints weight = 59984.335| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.37 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11000 Z= 0.245 Angle : 0.634 27.155 16944 Z= 0.357 Chirality : 0.056 1.914 2221 Planarity : 0.005 0.030 581 Dihedral : 26.302 176.460 6645 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 5.05 % Allowed : 34.34 % 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: 0.47 (0.88), residues: 114 helix: 1.53 (0.75), residues: 54 sheet: 0.29 (1.04), residues: 26 loop : -1.66 (1.31), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.012 0.002 TYR B 40 PHE 0.009 0.001 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.25 (11000) covalent geometry : angle 0.63365 / 0.36 (16944) hydrogen bonds : bond 0.08684 / 8.56 ( 400) hydrogen bonds : angle 2.78864 / 3.03 ( 749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2792.52 seconds wall clock time: 48 minutes 22.87 seconds (2902.87 seconds total)