Starting phenix.real_space_refine on Wed Aug 5 13:14:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zix_74287/08_2026/9zix_74287.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zix_74287/08_2026/9zix_74287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zix_74287/08_2026/9zix_74287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zix_74287/08_2026/9zix_74287.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zix_74287/08_2026/9zix_74287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zix_74287/08_2026/9zix_74287.map" } resolution = 3.68 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 3 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': 30, 'rna2p_pyr': 17, 'rna3p_pur': 213, 'rna3p_pyr': 157} Link IDs: {'rna2p': 47, 'rna3p': 369} 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: 2.14, per 1000 atoms: 0.22 Number of scatterers: 9933 At special positions: 0 Unit cell: (93.025, 170.037, 147.162, 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: 0.70 Conformation dependent library (CDL) restraints added in 69.6 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 51.7% alpha, 14.7% beta 135 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.533A pdb=" N ARG B 6 " --> pdb=" O LYS B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.102A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.535A pdb=" N VAL B 23 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 29 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 622 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1213 1.33 - 1.45: 5228 1.45 - 1.57: 3721 1.57 - 1.69: 833 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 271 " pdb=" C4 A A 271 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.43e+00 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.13e+00 bond pdb=" N9 G A 372 " pdb=" C4 G A 372 " ideal model delta sigma weight residual 1.375 1.391 -0.016 8.00e-03 1.56e+04 3.89e+00 bond pdb=" N9 A A 362 " pdb=" C4 A A 362 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.96e+00 bond pdb=" N9 G A 230 " pdb=" C4 G A 230 " ideal model delta sigma weight residual 1.375 1.389 -0.014 8.00e-03 1.56e+04 2.87e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15940 2.19 - 4.38: 974 4.38 - 6.57: 27 6.57 - 8.77: 1 8.77 - 10.96: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O2 C A 378 " pdb=" C2 C A 378 " pdb=" N3 C A 378 " ideal model delta sigma weight residual 121.90 115.56 6.34 7.00e-01 2.04e+00 8.20e+01 angle pdb=" N1 C A 378 " pdb=" C2 C A 378 " pdb=" O2 C A 378 " ideal model delta sigma weight residual 118.90 123.88 -4.98 6.00e-01 2.78e+00 6.89e+01 angle pdb=" O2 C A 194 " pdb=" C2 C A 194 " pdb=" N3 C A 194 " ideal model delta sigma weight residual 121.90 117.39 4.51 7.00e-01 2.04e+00 4.15e+01 angle pdb=" C PHE B 13 " pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 120.72 111.52 9.20 1.67e+00 3.59e-01 3.04e+01 angle pdb=" CA GLN B 14 " pdb=" CB GLN B 14 " pdb=" CG GLN B 14 " ideal model delta sigma weight residual 114.10 125.06 -10.96 2.00e+00 2.50e-01 3.00e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.76: 5805 33.76 - 67.52: 1144 67.52 - 101.28: 155 101.28 - 135.04: 7 135.04 - 168.80: 5 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' C A 207 " pdb=" C1' C A 207 " pdb=" N1 C A 207 " pdb=" C2 C A 207 " ideal model delta sinusoidal sigma weight residual 200.00 45.13 154.87 1 1.50e+01 4.44e-03 8.13e+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 -128.00 40.80 -168.80 1 1.70e+01 3.46e-03 6.58e+01 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 -37.27 -122.73 1 1.50e+01 4.44e-03 6.57e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1582 0.047 - 0.095: 217 0.095 - 0.142: 391 0.142 - 0.189: 27 0.189 - 0.237: 4 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CA GLN B 14 " pdb=" N GLN B 14 " pdb=" C GLN B 14 " pdb=" CB GLN B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C3' G A 122 " pdb=" C4' G A 122 " pdb=" O3' G A 122 " pdb=" C2' G A 122 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1' G A 372 " pdb=" O4' G A 372 " pdb=" C2' G A 372 " pdb=" N9 G A 372 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.21 2.00e-01 2.50e+01 1.05e+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 1.40e-02 5.86e+00 pdb=" N9 G A 298 " -0.033 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.009 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 " -0.002 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' G A 46 " -0.029 2.00e-02 2.50e+03 1.39e-02 5.80e+00 pdb=" N9 G A 46 " 0.037 2.00e-02 2.50e+03 pdb=" C8 G A 46 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 46 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 46 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 46 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G A 46 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G A 46 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 46 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 46 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 46 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G A 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 237 " 0.013 2.00e-02 2.50e+03 1.31e-02 5.16e+00 pdb=" N9 G A 237 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G A 237 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 237 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A 237 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 237 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G A 237 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 237 " 0.009 2.00e-02 2.50e+03 pdb=" C2 G A 237 " -0.034 2.00e-02 2.50e+03 pdb=" N2 G A 237 " 0.019 2.00e-02 2.50e+03 pdb=" N3 G A 237 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 237 " 0.000 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 52 2.51 - 3.11: 6856 3.11 - 3.71: 22179 3.71 - 4.30: 28055 4.30 - 4.90: 35284 Nonbonded interactions: 92426 Sorted by model distance: nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 509 " model vdw 1.918 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 506 " model vdw 1.941 2.170 nonbonded pdb=" OP2 C A 284 " pdb="MG MG A 521 " model vdw 1.964 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 509 " model vdw 1.967 2.170 nonbonded pdb=" OP1 A A 50 " pdb="MG MG A 503 " model vdw 1.979 2.170 ... (remaining 92421 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 group one per residue 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: 10.820 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.750 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 0.043 11000 Z= 0.278 Angle : 0.877 10.957 16944 Z= 0.785 Chirality : 0.063 0.237 2221 Planarity : 0.004 0.039 581 Dihedral : 26.548 168.799 6900 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.05 % Allowed : 35.35 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.86), residues: 114 helix: 1.13 (0.80), residues: 45 sheet: 2.38 (1.07), residues: 26 loop : -2.34 (1.03), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.005 0.001 TYR B 63 PHE 0.009 0.002 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.28 (11000) covalent geometry : angle 0.87712 / 0.79 (16944) hydrogen bonds : bond 0.12134 / 12.45 ( 395) hydrogen bonds : angle 4.65226 / 6.30 ( 745) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 GLU cc_start: 0.6856 (mp0) cc_final: 0.6247 (pm20) REVERT: B 27 GLN cc_start: 0.8037 (pm20) cc_final: 0.7738 (pm20) REVERT: B 92 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6914 (ptm) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.1168 time to fit residues: 4.1360 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 overall best weight: 7.9588 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.062564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039442 restraints weight = 91029.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.039273 restraints weight = 41570.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.039604 restraints weight = 30923.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.039604 restraints weight = 28553.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.039604 restraints weight = 28552.513| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11000 Z= 0.462 Angle : 1.029 11.965 16944 Z= 0.528 Chirality : 0.071 0.414 2221 Planarity : 0.007 0.052 581 Dihedral : 26.925 174.925 6654 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 46.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 11.11 % Allowed : 30.30 % 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: -0.55 (0.79), residues: 114 helix: 0.56 (0.76), residues: 47 sheet: 1.05 (0.93), residues: 26 loop : -2.48 (0.99), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.016 0.003 TYR B 63 PHE 0.017 0.003 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.46 (11000) covalent geometry : angle 1.02909 / 0.53 (16944) hydrogen bonds : bond 0.16198 / 17.02 ( 395) hydrogen bonds : angle 3.91527 / 5.42 ( 745) *********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.120 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 30 average time/residue: 0.1063 time to fit residues: 4.3488 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 LEU 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: 2.9990 chunk 35 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.062084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038917 restraints weight = 93343.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038474 restraints weight = 42159.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038886 restraints weight = 31971.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038963 restraints weight = 29432.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038963 restraints weight = 28426.172| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11000 Z= 0.419 Angle : 0.964 10.567 16944 Z= 0.507 Chirality : 0.063 0.309 2221 Planarity : 0.007 0.028 581 Dihedral : 27.414 178.749 6650 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 44.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 11.11 % Allowed : 29.29 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.73), residues: 114 helix: 0.09 (0.75), residues: 46 sheet: 0.11 (0.88), residues: 26 loop : -2.72 (0.86), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 65 TYR 0.009 0.002 TYR B 5 PHE 0.029 0.005 PHE B 28 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.42 (11000) covalent geometry : angle 0.96362 / 0.51 (16944) hydrogen bonds : bond 0.14314 / 14.60 ( 395) hydrogen bonds : angle 3.78313 / 5.09 ( 745) *********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8247 (mtm110) REVERT: B 92 MET cc_start: 0.8351 (mtm) cc_final: 0.7676 (mtp) outliers start: 11 outliers final: 7 residues processed: 29 average time/residue: 0.1265 time to fit residues: 4.9063 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 chunk 21 optimal weight: 50.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.062064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039470 restraints weight = 95048.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039154 restraints weight = 42183.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039323 restraints weight = 31363.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039323 restraints weight = 29110.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039323 restraints weight = 29110.615| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11000 Z= 0.347 Angle : 0.848 9.446 16944 Z= 0.459 Chirality : 0.058 0.284 2221 Planarity : 0.006 0.024 581 Dihedral : 27.336 172.509 6648 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 41.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 9.09 % Allowed : 38.38 % Favored : 52.53 % 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: -1.66 (0.72), residues: 114 helix: -0.26 (0.73), residues: 44 sheet: 0.05 (0.89), residues: 26 loop : -2.70 (0.86), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.016 0.002 TYR B 94 PHE 0.017 0.003 PHE B 28 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.35 (11000) covalent geometry : angle 0.84836 / 0.46 (16944) hydrogen bonds : bond 0.14312 / 14.51 ( 395) hydrogen bonds : angle 3.63388 / 4.85 ( 745) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8546 (mp-120) outliers start: 9 outliers final: 6 residues processed: 27 average time/residue: 0.1687 time to fit residues: 5.8306 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 LEU 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: 20.0000 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.062457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039760 restraints weight = 96622.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.039365 restraints weight = 44466.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039599 restraints weight = 33334.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039599 restraints weight = 30739.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039599 restraints weight = 30734.176| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11000 Z= 0.271 Angle : 0.738 8.974 16944 Z= 0.412 Chirality : 0.050 0.249 2221 Planarity : 0.006 0.021 581 Dihedral : 27.269 171.937 6648 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 33.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 9.09 % Allowed : 39.39 % Favored : 51.52 % 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: -1.44 (0.75), residues: 114 helix: -0.29 (0.75), residues: 50 sheet: 0.18 (0.87), residues: 26 loop : -2.63 (0.94), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 6 TYR 0.006 0.001 TYR B 81 PHE 0.006 0.002 PHE B 28 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.27 (11000) covalent geometry : angle 0.73766 / 0.41 (16944) hydrogen bonds : bond 0.12376 / 12.44 ( 395) hydrogen bonds : angle 3.42661 / 4.53 ( 745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 GLU cc_start: 0.9111 (mp0) cc_final: 0.8911 (pm20) outliers start: 9 outliers final: 9 residues processed: 27 average time/residue: 0.1268 time to fit residues: 4.5947 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 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: 30.0000 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.064243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041811 restraints weight = 102606.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043181 restraints weight = 40876.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043181 restraints weight = 31819.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043181 restraints weight = 31819.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043181 restraints weight = 31819.487| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11000 Z= 0.396 Angle : 0.909 10.384 16944 Z= 0.483 Chirality : 0.061 0.308 2221 Planarity : 0.007 0.026 581 Dihedral : 27.397 172.945 6648 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 47.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 10.10 % Allowed : 35.35 % Favored : 54.55 % 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: -2.12 (0.69), residues: 114 helix: -0.45 (0.72), residues: 44 sheet: -0.41 (0.83), residues: 26 loop : -3.05 (0.80), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.009 0.002 TYR B 63 PHE 0.018 0.003 PHE B 28 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.40 (11000) covalent geometry : angle 0.90895 / 0.48 (16944) hydrogen bonds : bond 0.15369 / 15.56 ( 395) hydrogen bonds : angle 3.64901 / 4.87 ( 745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.7063 (mtp) cc_final: 0.6833 (mtp) outliers start: 10 outliers final: 8 residues processed: 28 average time/residue: 0.1257 time to fit residues: 4.7700 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037082 restraints weight = 97418.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.037388 restraints weight = 47308.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037708 restraints weight = 37488.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037708 restraints weight = 34106.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037708 restraints weight = 34106.115| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11000 Z= 0.537 Angle : 1.243 14.695 16944 Z= 0.625 Chirality : 0.080 0.384 2221 Planarity : 0.008 0.050 581 Dihedral : 27.850 173.439 6648 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 67.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 10.10 % Allowed : 37.37 % Favored : 52.53 % 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: -2.93 (0.70), residues: 114 helix: -1.18 (0.70), residues: 50 sheet: -0.97 (0.88), residues: 25 loop : -3.53 (0.80), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.018 0.003 TYR B 63 PHE 0.032 0.005 PHE B 28 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.54 (11000) covalent geometry : angle 1.24276 / 0.62 (16944) hydrogen bonds : bond 0.19455 / 19.73 ( 395) hydrogen bonds : angle 4.15555 / 5.43 ( 745) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7819 (p) REVERT: B 73 GLU cc_start: 0.9295 (tp30) cc_final: 0.9029 (tm-30) outliers start: 10 outliers final: 7 residues processed: 27 average time/residue: 0.1451 time to fit residues: 5.2418 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 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: 20.0000 chunk 26 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 36 optimal weight: 40.0000 overall best weight: 10.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN B 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.060248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036538 restraints weight = 97883.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.036891 restraints weight = 48765.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037034 restraints weight = 38373.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037034 restraints weight = 36765.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037034 restraints weight = 36765.700| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 11000 Z= 0.546 Angle : 1.188 14.939 16944 Z= 0.606 Chirality : 0.078 0.414 2221 Planarity : 0.008 0.034 581 Dihedral : 28.007 174.447 6648 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 63.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 11.11 % Allowed : 36.36 % Favored : 52.53 % 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: -3.11 (0.71), residues: 114 helix: -1.01 (0.72), residues: 45 sheet: -1.42 (0.85), residues: 29 loop : -3.72 (0.87), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG B 62 TYR 0.014 0.003 TYR B 81 PHE 0.028 0.006 PHE B 17 HIS 0.007 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.55 (11000) covalent geometry : angle 1.18810 / 0.61 (16944) hydrogen bonds : bond 0.19011 / 18.96 ( 395) hydrogen bonds : angle 4.04333 / 5.25 ( 745) *********************** 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 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.7727 (mtm-85) REVERT: B 92 MET cc_start: 0.7456 (mtp) cc_final: 0.7232 (mtp) outliers start: 11 outliers final: 8 residues processed: 30 average time/residue: 0.1374 time to fit residues: 5.4166 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 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: 20.0000 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 12 optimal weight: 40.0000 chunk 48 optimal weight: 5.9990 overall best weight: 5.5994 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.060973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.037780 restraints weight = 96598.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038095 restraints weight = 43310.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038450 restraints weight = 32887.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038450 restraints weight = 30569.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038450 restraints weight = 30569.510| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11000 Z= 0.322 Angle : 0.861 12.021 16944 Z= 0.481 Chirality : 0.058 0.395 2221 Planarity : 0.007 0.035 581 Dihedral : 27.747 174.658 6648 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 45.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 7.07 % Allowed : 39.39 % Favored : 53.54 % 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: -2.52 (0.75), residues: 114 helix: -0.36 (0.77), residues: 44 sheet: -1.09 (0.87), residues: 28 loop : -3.51 (0.88), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 6 TYR 0.012 0.002 TYR B 81 PHE 0.013 0.002 PHE B 17 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.32 (11000) covalent geometry : angle 0.86140 / 0.48 (16944) hydrogen bonds : bond 0.15382 / 15.29 ( 395) hydrogen bonds : angle 3.63498 / 4.80 ( 745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.7716 (mtp) cc_final: 0.7292 (mtp) outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.1445 time to fit residues: 5.1847 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 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: 4.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 12 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.060638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037869 restraints weight = 95268.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038101 restraints weight = 43753.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038456 restraints weight = 33768.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038456 restraints weight = 31918.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038456 restraints weight = 31910.436| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11000 Z= 0.390 Angle : 0.973 15.280 16944 Z= 0.514 Chirality : 0.066 0.391 2221 Planarity : 0.007 0.069 581 Dihedral : 27.729 174.501 6648 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 51.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.08 % Allowed : 38.38 % Favored : 53.54 % 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: -2.64 (0.71), residues: 114 helix: -0.65 (0.73), residues: 44 sheet: -1.05 (0.86), residues: 28 loop : -3.42 (0.83), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 6 TYR 0.008 0.002 TYR B 63 PHE 0.016 0.003 PHE B 28 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.39 (11000) covalent geometry : angle 0.97270 / 0.51 (16944) hydrogen bonds : bond 0.16002 / 16.04 ( 395) hydrogen bonds : angle 3.71600 / 4.92 ( 745) ********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 29 average time/residue: 0.1370 time to fit residues: 5.2546 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.063562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041708 restraints weight = 101904.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.042609 restraints weight = 41086.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.043481 restraints weight = 32158.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.043932 restraints weight = 27724.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.044048 restraints weight = 25761.072| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11000 Z= 0.325 Angle : 0.867 12.932 16944 Z= 0.470 Chirality : 0.059 0.376 2221 Planarity : 0.006 0.030 581 Dihedral : 27.604 175.250 6648 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 44.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 8.08 % Allowed : 39.39 % Favored : 52.53 % 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: -2.65 (0.70), residues: 114 helix: -0.65 (0.70), residues: 45 sheet: -0.99 (0.85), residues: 28 loop : -3.56 (0.83), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 57 TYR 0.011 0.002 TYR B 94 PHE 0.015 0.003 PHE B 28 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.33 (11000) covalent geometry : angle 0.86708 / 0.47 (16944) hydrogen bonds : bond 0.14514 / 14.61 ( 395) hydrogen bonds : angle 3.46414 / 4.69 ( 745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.59 seconds wall clock time: 43 minutes 33.80 seconds (2613.80 seconds total)