Starting phenix.real_space_refine on Wed Aug 5 13:08:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zin_74280/08_2026/9zin_74280.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zin_74280/08_2026/9zin_74280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zin_74280/08_2026/9zin_74280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zin_74280/08_2026/9zin_74280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zin_74280/08_2026/9zin_74280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zin_74280/08_2026/9zin_74280.map" } resolution = 3.25 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 29 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 4 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: 9938 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': 24, 'rna2p_pyr': 17, 'rna3p_pur': 219, 'rna3p_pyr': 157} Link IDs: {'rna2p': 41, 'rna3p': 375} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Unusual residues: {' MG': 29} Classifications: {'undetermined': 29} Link IDs: {None: 28} Time building chain proxies: 2.56, per 1000 atoms: 0.26 Number of scatterers: 9938 At special positions: 0 Unit cell: (122.976, 169.092, 146.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 3 16.00 P 417 15.00 Mg 29 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: 0.81 Conformation dependent library (CDL) restraints added in 55.4 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: 5 helices and 1 sheets defined 49.1% alpha, 17.2% beta 144 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.609A pdb=" N ARG B 6 " --> pdb=" O LYS B 3 " (cutoff:3.500A) 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 92 removed outlier: 3.600A pdb=" N GLU B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.567A pdb=" N ALA B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.592A pdb=" N LEU B 33 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 42 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 85 " --> pdb=" O SER B 46 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1244 1.33 - 1.45: 5216 1.45 - 1.57: 3702 1.57 - 1.69: 833 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 G A 372 " pdb=" C4 G A 372 " ideal model delta sigma weight residual 1.375 1.389 -0.014 8.00e-03 1.56e+04 2.96e+00 bond pdb=" N9 A A 151 " pdb=" C4 A A 151 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.93e+00 bond pdb=" C2 G A 32 " pdb=" N3 G A 32 " ideal model delta sigma weight residual 1.323 1.310 0.013 8.00e-03 1.56e+04 2.77e+00 bond pdb=" N9 A A 189 " pdb=" C4 A A 189 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.68e+00 bond pdb=" C8 A A 412 " pdb=" N7 A A 412 " ideal model delta sigma weight residual 1.311 1.301 0.010 7.00e-03 2.04e+04 2.09e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 15660 1.88 - 3.75: 1246 3.75 - 5.63: 32 5.63 - 7.51: 5 7.51 - 9.38: 1 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O2 C A 366 " pdb=" C2 C A 366 " pdb=" N3 C A 366 " ideal model delta sigma weight residual 121.90 117.36 4.54 7.00e-01 2.04e+00 4.21e+01 angle pdb=" O2 C A 184 " pdb=" C2 C A 184 " pdb=" N3 C A 184 " ideal model delta sigma weight residual 121.90 117.36 4.54 7.00e-01 2.04e+00 4.21e+01 angle pdb=" N1 C A 184 " pdb=" C2 C A 184 " pdb=" O2 C A 184 " ideal model delta sigma weight residual 118.90 122.20 -3.30 6.00e-01 2.78e+00 3.03e+01 angle pdb=" O4' G A 32 " pdb=" C1' G A 32 " pdb=" N9 G A 32 " ideal model delta sigma weight residual 108.20 103.92 4.28 8.00e-01 1.56e+00 2.86e+01 angle pdb=" O5' G A 32 " pdb=" C5' G A 32 " pdb=" C4' G A 32 " ideal model delta sigma weight residual 109.40 113.20 -3.80 8.00e-01 1.56e+00 2.26e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.44: 5887 32.44 - 64.88: 1070 64.88 - 97.31: 146 97.31 - 129.75: 9 129.75 - 162.19: 4 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual -160.00 -8.88 -151.12 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U A 371 " pdb=" C1' U A 371 " pdb=" N1 U A 371 " pdb=" C2 U A 371 " ideal model delta sinusoidal sigma weight residual -160.00 -59.28 -100.72 1 1.50e+01 4.44e-03 5.06e+01 dihedral pdb=" O4' U A 33 " pdb=" C1' U A 33 " pdb=" N1 U A 33 " pdb=" C2 U A 33 " ideal model delta sinusoidal sigma weight residual -128.00 -68.84 -59.16 1 1.70e+01 3.46e-03 1.62e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1564 0.044 - 0.089: 220 0.089 - 0.133: 272 0.133 - 0.178: 159 0.178 - 0.222: 6 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CA GLU B 96 " pdb=" N GLU B 96 " pdb=" C GLU B 96 " pdb=" CB GLU B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' G A 345 " pdb=" C4' G A 345 " pdb=" O3' G A 345 " pdb=" C2' G A 345 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.21 2.00e-01 2.50e+01 1.15e+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 1.13e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.033 2.00e-02 2.50e+03 1.41e-02 5.93e+00 pdb=" N9 G A 298 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 184 " 0.016 2.00e-02 2.50e+03 1.42e-02 4.53e+00 pdb=" N1 C A 184 " -0.019 2.00e-02 2.50e+03 pdb=" C2 C A 184 " 0.024 2.00e-02 2.50e+03 pdb=" O2 C A 184 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C A 184 " -0.008 2.00e-02 2.50e+03 pdb=" C4 C A 184 " 0.014 2.00e-02 2.50e+03 pdb=" N4 C A 184 " -0.000 2.00e-02 2.50e+03 pdb=" C5 C A 184 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C A 184 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 32 " -0.029 2.00e-02 2.50e+03 1.21e-02 4.40e+00 pdb=" N9 G A 32 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G A 32 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 32 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 32 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 32 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G A 32 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G A 32 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A 32 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G A 32 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 32 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G A 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 56 2.55 - 3.13: 7090 3.13 - 3.72: 20882 3.72 - 4.31: 27327 4.31 - 4.90: 34985 Nonbonded interactions: 90340 Sorted by model distance: nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 510 " model vdw 1.956 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 510 " model vdw 1.971 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 511 " model vdw 1.995 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 507 " model vdw 2.002 2.170 nonbonded pdb=" OP1 A A 50 " pdb="MG MG A 504 " model vdw 2.015 2.170 ... (remaining 90335 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: 9.090 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 0.037 11000 Z= 0.229 Angle : 0.831 9.384 16944 Z= 0.700 Chirality : 0.063 0.222 2221 Planarity : 0.004 0.025 581 Dihedral : 25.349 162.190 6900 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.26 % Favored : 93.86 % Rotamer: Outliers : 3.03 % Allowed : 33.33 % 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: -0.10 (0.86), residues: 114 helix: 1.72 (0.83), residues: 46 sheet: -0.29 (1.00), residues: 28 loop : -2.06 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.008 0.001 TYR B 31 PHE 0.008 0.002 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.23 (11000) covalent geometry : angle 0.83125 / 0.70 (16944) hydrogen bonds : bond 0.08873 / 8.01 ( 415) hydrogen bonds : angle 3.90305 / 4.46 ( 765) *********************** 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 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.152 Fit side-chains REVERT: B 91 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8109 (mm-30) outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.0799 time to fit residues: 2.5852 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER 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: 0.9980 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.089093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048986 restraints weight = 58781.123| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.79 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 11000 Z= 0.466 Angle : 0.855 8.968 16944 Z= 0.442 Chirality : 0.058 0.372 2221 Planarity : 0.007 0.045 581 Dihedral : 25.512 165.679 6646 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.77 % Favored : 90.35 % Rotamer: Outliers : 11.11 % Allowed : 25.25 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.79), residues: 114 helix: 0.29 (0.73), residues: 48 sheet: -0.57 (1.03), residues: 31 loop : -2.42 (0.96), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B 106 TYR 0.015 0.003 TYR B 31 PHE 0.014 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.47 (11000) covalent geometry : angle 0.85487 / 0.44 (16944) hydrogen bonds : bond 0.11863 / 12.27 ( 415) hydrogen bonds : angle 3.18346 / 3.83 ( 765) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 14 time to evaluate : 0.141 Fit side-chains REVERT: B 91 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8548 (mm-30) REVERT: B 92 MET cc_start: 0.8841 (ttm) cc_final: 0.8452 (mtp) outliers start: 11 outliers final: 4 residues processed: 22 average time/residue: 0.0731 time to fit residues: 2.6774 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.087435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048176 restraints weight = 58606.135| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.81 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2967 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= 0.497 Angle : 0.963 10.075 16944 Z= 0.492 Chirality : 0.065 0.380 2221 Planarity : 0.007 0.025 581 Dihedral : 25.999 164.651 6645 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 29.50 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.77 % Favored : 90.35 % Rotamer: Outliers : 11.11 % Allowed : 27.27 % 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: -2.11 (0.75), residues: 114 helix: -0.71 (0.66), residues: 48 sheet: -0.19 (1.25), residues: 25 loop : -2.98 (0.82), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 106 TYR 0.023 0.004 TYR B 31 PHE 0.012 0.003 PHE B 13 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.50 (11000) covalent geometry : angle 0.96281 / 0.49 (16944) hydrogen bonds : bond 0.12993 / 13.81 ( 415) hydrogen bonds : angle 3.32099 / 4.07 ( 765) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.095 Fit side-chains REVERT: B 19 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: B 91 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8617 (mm-30) REVERT: B 92 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8233 (mtp) outliers start: 11 outliers final: 4 residues processed: 23 average time/residue: 0.1285 time to fit residues: 4.0389 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 : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET 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 51 optimal weight: 1.9990 chunk 22 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.087164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.047310 restraints weight = 55666.643| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.34 r_work: 0.2728 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 11000 Z= 0.409 Angle : 0.814 9.708 16944 Z= 0.430 Chirality : 0.056 0.381 2221 Planarity : 0.006 0.039 581 Dihedral : 26.009 162.625 6645 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.65 % Favored : 89.47 % Rotamer: Outliers : 7.07 % Allowed : 34.34 % Favored : 58.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.78), residues: 114 helix: -0.11 (0.71), residues: 48 sheet: -0.61 (1.20), residues: 26 loop : -2.89 (0.87), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.018 0.003 TYR B 31 PHE 0.008 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.41 (11000) covalent geometry : angle 0.81429 / 0.43 (16944) hydrogen bonds : bond 0.11805 / 12.48 ( 415) hydrogen bonds : angle 3.16653 / 3.94 ( 765) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.086 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 20 average time/residue: 0.0575 time to fit residues: 1.8599 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 40.0000 chunk 23 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.085864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046108 restraints weight = 56079.628| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.24 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 11000 Z= 0.603 Angle : 1.107 11.518 16944 Z= 0.548 Chirality : 0.073 0.414 2221 Planarity : 0.007 0.040 581 Dihedral : 26.213 164.367 6645 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 35.91 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.40 % Favored : 87.72 % Rotamer: Outliers : 11.11 % Allowed : 28.28 % 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: -2.73 (0.74), residues: 114 helix: -0.91 (0.64), residues: 48 sheet: -1.14 (1.19), residues: 26 loop : -3.31 (0.85), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 106 TYR 0.020 0.003 TYR B 31 PHE 0.009 0.003 PHE B 41 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.60 (11000) covalent geometry : angle 1.10724 / 0.55 (16944) hydrogen bonds : bond 0.15042 / 15.98 ( 415) hydrogen bonds : angle 3.57013 / 4.39 ( 765) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 15 time to evaluate : 0.122 Fit side-chains REVERT: B 19 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: B 92 MET cc_start: 0.9018 (ttm) cc_final: 0.8206 (mtp) outliers start: 11 outliers final: 6 residues processed: 23 average time/residue: 0.0784 time to fit residues: 2.6107 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 50.0000 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.087561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.047935 restraints weight = 56050.013| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.11 r_work: 0.2756 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3429 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= 0.228 Angle : 0.637 9.425 16944 Z= 0.370 Chirality : 0.044 0.354 2221 Planarity : 0.005 0.025 581 Dihedral : 26.079 161.857 6645 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.14 % Favored : 92.98 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.82), residues: 114 helix: 0.59 (0.79), residues: 48 sheet: -0.97 (1.16), residues: 26 loop : -3.09 (0.86), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.016 0.002 TYR B 31 PHE 0.010 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.23 (11000) covalent geometry : angle 0.63740 / 0.37 (16944) hydrogen bonds : bond 0.10341 / 10.90 ( 415) hydrogen bonds : angle 2.97026 / 3.57 ( 765) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.095 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 21 average time/residue: 0.0983 time to fit residues: 3.0510 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 40.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 43 optimal weight: 0.0000 chunk 36 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 16 optimal weight: 50.0000 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.087698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048744 restraints weight = 55964.181| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.20 r_work: 0.2761 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11000 Z= 0.234 Angle : 0.620 8.525 16944 Z= 0.352 Chirality : 0.043 0.337 2221 Planarity : 0.005 0.033 581 Dihedral : 25.845 162.354 6645 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.14 % Favored : 92.98 % 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: -1.18 (0.85), residues: 114 helix: 0.81 (0.81), residues: 48 sheet: -0.03 (1.25), residues: 22 loop : -3.11 (0.92), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.018 0.002 TYR B 31 PHE 0.009 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.23 (11000) covalent geometry : angle 0.62021 / 0.35 (16944) hydrogen bonds : bond 0.09511 / 9.88 ( 415) hydrogen bonds : angle 2.80641 / 3.32 ( 765) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.143 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 0.0895 time to fit residues: 3.1272 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 20.0000 chunk 16 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 5.7190 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.086423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.047005 restraints weight = 55339.228| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.56 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11000 Z= 0.418 Angle : 0.826 9.321 16944 Z= 0.434 Chirality : 0.058 0.382 2221 Planarity : 0.006 0.039 581 Dihedral : 26.005 164.986 6645 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.77 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 32.32 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.78), residues: 114 helix: 0.09 (0.75), residues: 48 sheet: -0.92 (1.14), residues: 25 loop : -3.44 (0.83), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.019 0.003 TYR B 31 PHE 0.008 0.002 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.42 (11000) covalent geometry : angle 0.82563 / 0.43 (16944) hydrogen bonds : bond 0.11909 / 12.56 ( 415) hydrogen bonds : angle 3.12592 / 3.76 ( 765) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.149 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.0832 time to fit residues: 2.6910 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 overall best weight: 5.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.086441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047032 restraints weight = 56069.156| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.49 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11000 Z= 0.411 Angle : 0.807 9.536 16944 Z= 0.427 Chirality : 0.056 0.377 2221 Planarity : 0.006 0.031 581 Dihedral : 26.059 164.405 6645 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.53 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 32.32 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.79), residues: 114 helix: 0.21 (0.77), residues: 48 sheet: -1.04 (1.14), residues: 25 loop : -3.54 (0.82), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.017 0.003 TYR B 31 PHE 0.010 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.41 (11000) covalent geometry : angle 0.80711 / 0.43 (16944) hydrogen bonds : bond 0.11502 / 12.13 ( 415) hydrogen bonds : angle 3.08196 / 3.73 ( 765) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.157 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.0936 time to fit residues: 2.9811 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 2.4982 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.087678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048177 restraints weight = 55087.606| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.14 r_work: 0.2764 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.3660 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= 0.210 Angle : 0.595 8.571 16944 Z= 0.347 Chirality : 0.042 0.337 2221 Planarity : 0.005 0.031 581 Dihedral : 25.948 163.020 6645 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.89 % Favored : 91.23 % Rotamer: Outliers : 4.04 % Allowed : 33.33 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.84), residues: 114 helix: 0.87 (0.82), residues: 48 sheet: -0.23 (1.23), residues: 22 loop : -3.24 (0.89), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 35 TYR 0.016 0.002 TYR B 31 PHE 0.009 0.002 PHE B 41 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.21 (11000) covalent geometry : angle 0.59538 / 0.35 (16944) hydrogen bonds : bond 0.09362 / 9.67 ( 415) hydrogen bonds : angle 2.80620 / 3.29 ( 765) ********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.111 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 21 average time/residue: 0.0784 time to fit residues: 2.4258 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 chunk 37 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.087486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048455 restraints weight = 56134.938| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.31 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11000 Z= 0.226 Angle : 0.606 8.430 16944 Z= 0.348 Chirality : 0.043 0.342 2221 Planarity : 0.005 0.029 581 Dihedral : 25.903 163.745 6645 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.02 % Favored : 92.11 % Rotamer: Outliers : 1.01 % Allowed : 36.36 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.85), residues: 114 helix: 0.86 (0.81), residues: 48 sheet: -0.00 (1.25), residues: 22 loop : -3.17 (0.90), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 106 TYR 0.015 0.002 TYR B 31 PHE 0.009 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.23 (11000) covalent geometry : angle 0.60583 / 0.35 (16944) hydrogen bonds : bond 0.09481 / 9.81 ( 415) hydrogen bonds : angle 2.81087 / 3.31 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3471.86 seconds wall clock time: 59 minutes 53.02 seconds (3593.02 seconds total)