Starting phenix.real_space_refine on Wed Aug 5 13:11:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zic_74269/08_2026/9zic_74269.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zic_74269/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9zic_74269/08_2026/9zic_74269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zic_74269/08_2026/9zic_74269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zic_74269/08_2026/9zic_74269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zic_74269/08_2026/9zic_74269.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 417 5.49 5 Mg 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-2.2rc3-6140/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: 2.24, per 1000 atoms: 0.23 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: 0.77 Conformation dependent library (CDL) restraints added in 67.7 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: 1.61 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: 2.42 Time building geometry restraints manager: 1.11 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=" 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 1.10e+00 8.26e-01 3.98e+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 ... (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 2.47 2.24 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C1' A A 50 " pdb=" O4' A A 50 " pdb=" C2' A A 50 " pdb=" N9 A A 50 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.09e+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: 9.600 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.850 ------------------------------------------------------------------------------- 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= 0.284 Angle : 0.890 26.976 16944 Z= 0.700 Chirality : 0.076 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 0.00303 / 0.28 (11000) covalent geometry : angle 0.89004 / 0.70 (16944) hydrogen bonds : bond 0.10413 / 11.29 ( 400) hydrogen bonds : angle 3.77819 / 3.91 ( 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 : 0.152 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0784 time to fit residues: 2.1620 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 : 0.145 ------------------------------------------------------------------------------- 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: 20.0000 chunk 48 optimal weight: 0.0870 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 overall best weight: 6.2166 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.085735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052264 restraints weight = 59819.062| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.49 r_work: 0.2627 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 11000 Z= 0.456 Angle : 0.916 26.158 16944 Z= 0.456 Chirality : 0.072 1.820 2221 Planarity : 0.006 0.038 581 Dihedral : 25.841 176.782 6645 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 28.28 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.79), residues: 114 helix: 0.73 (0.65), residues: 48 sheet: 0.42 (1.02), residues: 26 loop : -1.56 (1.13), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.011 0.002 TYR B 31 PHE 0.019 0.004 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.46 (11000) covalent geometry : angle 0.91605 / 0.46 (16944) hydrogen bonds : bond 0.11927 / 12.87 ( 400) hydrogen bonds : angle 2.94323 / 3.38 ( 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.126 Fit side-chains REVERT: B 92 MET cc_start: 0.8947 (ttt) cc_final: 0.8711 (ttt) outliers start: 6 outliers final: 3 residues processed: 18 average time/residue: 0.0861 time to fit residues: 2.3610 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 overall best weight: 5.3586 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.085294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047107 restraints weight = 59909.702| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.48 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 11000 Z= 0.373 Angle : 0.819 25.988 16944 Z= 0.416 Chirality : 0.066 1.841 2221 Planarity : 0.005 0.025 581 Dihedral : 26.076 177.038 6645 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 29.29 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.84), residues: 114 helix: 1.03 (0.74), residues: 53 sheet: -0.09 (0.98), residues: 26 loop : -1.55 (1.25), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 6 TYR 0.020 0.003 TYR B 40 PHE 0.018 0.003 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.37 (11000) covalent geometry : angle 0.81854 / 0.42 (16944) hydrogen bonds : bond 0.10833 / 11.85 ( 400) hydrogen bonds : angle 2.90315 / 3.34 ( 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: 5 poor density : 13 time to evaluate : 0.155 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.0766 time to fit residues: 2.0473 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 48 SER 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: 20.0000 chunk 17 optimal weight: 50.0000 chunk 50 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 chunk 21 optimal weight: 50.0000 overall best weight: 8.3392 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.083781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044805 restraints weight = 60001.609| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.20 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 11000 Z= 0.616 Angle : 1.067 26.194 16944 Z= 0.524 Chirality : 0.079 1.815 2221 Planarity : 0.007 0.033 581 Dihedral : 26.282 177.516 6645 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 30.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 7.07 % Allowed : 30.30 % 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: -0.82 (0.80), residues: 114 helix: 0.39 (0.70), residues: 53 sheet: -0.57 (0.93), residues: 26 loop : -1.84 (1.22), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.023 0.003 TYR B 40 PHE 0.022 0.004 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01019 / 0.62 (11000) covalent geometry : angle 1.06665 / 0.52 (16944) hydrogen bonds : bond 0.15067 / 16.62 ( 400) hydrogen bonds : angle 3.31397 / 3.98 ( 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: 7 poor density : 11 time to evaluate : 0.142 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 15 average time/residue: 0.0752 time to fit residues: 1.9003 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE 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 74 GLU 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: 10.0000 chunk 3 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.085038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.045708 restraints weight = 60096.220| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.19 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11000 Z= 0.270 Angle : 0.723 26.338 16944 Z= 0.381 Chirality : 0.060 1.851 2221 Planarity : 0.005 0.027 581 Dihedral : 26.228 176.720 6645 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: 0.07 (0.87), residues: 114 helix: 1.22 (0.74), residues: 54 sheet: -0.02 (1.02), residues: 26 loop : -1.76 (1.31), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.014 0.002 TYR B 40 PHE 0.014 0.002 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.27 (11000) covalent geometry : angle 0.72291 / 0.38 (16944) hydrogen bonds : bond 0.10305 / 11.27 ( 400) hydrogen bonds : angle 2.85565 / 3.30 ( 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: 7 poor density : 13 time to evaluate : 0.147 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 17 average time/residue: 0.0991 time to fit residues: 2.5418 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER 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: 9.9990 chunk 16 optimal weight: 50.0000 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 overall best weight: 6.5190 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.084071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044485 restraints weight = 60079.803| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.85 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 11000 Z= 0.468 Angle : 0.908 26.449 16944 Z= 0.455 Chirality : 0.070 1.826 2221 Planarity : 0.006 0.028 581 Dihedral : 26.257 176.822 6645 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 10.10 % Allowed : 27.27 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.84), residues: 114 helix: 0.76 (0.71), residues: 54 sheet: -0.22 (0.99), residues: 26 loop : -1.96 (1.29), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.016 0.002 TYR B 40 PHE 0.016 0.003 PHE B 13 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.47 (11000) covalent geometry : angle 0.90778 / 0.45 (16944) hydrogen bonds : bond 0.12487 / 13.66 ( 400) hydrogen bonds : angle 3.11942 / 3.67 ( 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.146 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 20 average time/residue: 0.0720 time to fit residues: 2.3798 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE 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 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 VAL 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: 8.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.083533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044314 restraints weight = 59790.527| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.90 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 11000 Z= 0.479 Angle : 0.965 26.536 16944 Z= 0.482 Chirality : 0.073 1.814 2221 Planarity : 0.007 0.038 581 Dihedral : 26.420 176.518 6645 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 29.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % 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: -0.84 (0.80), residues: 114 helix: 0.44 (0.67), residues: 53 sheet: -0.49 (0.93), residues: 26 loop : -2.05 (1.24), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 57 TYR 0.020 0.003 TYR B 5 PHE 0.016 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.48 (11000) covalent geometry : angle 0.96472 / 0.48 (16944) hydrogen bonds : bond 0.13173 / 14.55 ( 400) hydrogen bonds : angle 3.24185 / 3.76 ( 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 13 time to evaluate : 0.145 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 20 average time/residue: 0.0889 time to fit residues: 2.7391 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE 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 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 VAL 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: 10.0000 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.082128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042213 restraints weight = 57177.151| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.88 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.131 11000 Z= 0.769 Angle : 1.383 26.792 16944 Z= 0.646 Chirality : 0.094 1.750 2221 Planarity : 0.008 0.041 581 Dihedral : 26.665 177.155 6645 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 42.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 10.10 % Allowed : 34.34 % Favored : 55.56 % 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: -1.61 (0.77), residues: 114 helix: -0.19 (0.65), residues: 54 sheet: -0.94 (0.91), residues: 26 loop : -2.41 (1.21), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG B 86 TYR 0.022 0.004 TYR B 40 PHE 0.027 0.005 PHE B 13 HIS 0.008 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01269 / 0.77 (11000) covalent geometry : angle 1.38256 / 0.65 (16944) hydrogen bonds : bond 0.17676 / 19.69 ( 400) hydrogen bonds : angle 3.73522 / 4.43 ( 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 11 time to evaluate : 0.146 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 19 average time/residue: 0.0683 time to fit residues: 2.2170 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 9 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 21 VAL 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 48 SER Chi-restraints excluded: chain B residue 104 VAL 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: 1.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 15 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.083767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046297 restraints weight = 59809.775| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.44 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11000 Z= 0.325 Angle : 0.810 26.757 16944 Z= 0.424 Chirality : 0.064 1.827 2221 Planarity : 0.006 0.039 581 Dihedral : 26.563 175.954 6645 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 6.06 % Allowed : 38.38 % Favored : 55.56 % 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: -0.48 (0.83), residues: 114 helix: 0.88 (0.70), residues: 54 sheet: -0.56 (0.95), residues: 26 loop : -1.97 (1.30), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.015 0.002 TYR B 40 PHE 0.015 0.002 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.33 (11000) covalent geometry : angle 0.80956 / 0.42 (16944) hydrogen bonds : bond 0.11551 / 12.79 ( 400) hydrogen bonds : angle 3.11279 / 3.53 ( 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 : 0.104 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 19 average time/residue: 0.0900 time to fit residues: 2.6321 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 : 0.133 ------------------------------------------------------------------------------- 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 48 SER Chi-restraints excluded: chain B residue 104 VAL 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: 0.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 40.0000 chunk 45 optimal weight: 0.4980 overall best weight: 3.8386 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.084136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.044899 restraints weight = 59062.753| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.27 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11000 Z= 0.304 Angle : 0.758 26.466 16944 Z= 0.390 Chirality : 0.062 1.836 2221 Planarity : 0.005 0.038 581 Dihedral : 26.324 173.206 6645 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 5.05 % Allowed : 39.39 % Favored : 55.56 % 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: 0.06 (0.86), residues: 114 helix: 1.18 (0.75), residues: 54 sheet: 0.01 (0.98), residues: 26 loop : -1.76 (1.31), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.012 0.002 TYR B 40 PHE 0.013 0.002 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.30 (11000) covalent geometry : angle 0.75790 / 0.39 (16944) hydrogen bonds : bond 0.09519 / 10.21 ( 400) hydrogen bonds : angle 2.92854 / 3.27 ( 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 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.147 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 16 average time/residue: 0.0933 time to fit residues: 2.2039 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 : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 104 VAL 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: 4.9990 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 12 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.084401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.045703 restraints weight = 59796.775| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.15 r_work: 0.2657 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11000 Z= 0.258 Angle : 0.710 26.498 16944 Z= 0.371 Chirality : 0.059 1.854 2221 Planarity : 0.005 0.036 581 Dihedral : 26.236 172.870 6645 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.05 % Allowed : 39.39 % Favored : 55.56 % 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 (0.87), residues: 114 helix: 1.38 (0.75), residues: 54 sheet: 0.20 (1.03), residues: 26 loop : -1.52 (1.32), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.014 0.002 TYR B 40 PHE 0.017 0.002 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.26 (11000) covalent geometry : angle 0.71040 / 0.37 (16944) hydrogen bonds : bond 0.09193 / 9.97 ( 400) hydrogen bonds : angle 2.84156 / 3.08 ( 749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.32 seconds wall clock time: 59 minutes 6.89 seconds (3546.89 seconds total)