Starting phenix.real_space_refine on Wed Aug 5 13:07:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zik_74277/08_2026/9zik_74277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zik_74277/08_2026/9zik_74277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zik_74277/08_2026/9zik_74277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zik_74277/08_2026/9zik_74277.map" model { file = "/net/cci-nas-00/data/ceres_data/9zik_74277/08_2026/9zik_74277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zik_74277/08_2026/9zik_74277.cif" } resolution = 3.33 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= 0.006 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 27 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 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: 9936 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 18, 'rna3p_pur': 218, 'rna3p_pyr': 156} Link IDs: {'rna2p': 43, 'rna3p': 373} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Unusual residues: {' MG': 27} Classifications: {'undetermined': 27} Link IDs: {None: 26} Time building chain proxies: 2.27, per 1000 atoms: 0.23 Number of scatterers: 9936 At special positions: 0 Unit cell: (91.5, 174.948, 147.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 3 16.00 P 417 15.00 Mg 27 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: 0.73 Conformation dependent library (CDL) restraints added in 66.0 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 45.7% alpha, 14.7% beta 142 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.744A pdb=" N LEU B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 93 through 109 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.600A pdb=" N ASP B 80 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 632 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1059 1.33 - 1.45: 5220 1.45 - 1.56: 3883 1.56 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" C2 G A 32 " pdb=" N3 G A 32 " ideal model delta sigma weight residual 1.323 1.308 0.015 8.00e-03 1.56e+04 3.31e+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 3.28e+00 bond pdb=" C6 A A 257 " pdb=" N1 A A 257 " ideal model delta sigma weight residual 1.351 1.339 0.012 7.00e-03 2.04e+04 3.08e+00 bond pdb=" N9 G A 32 " pdb=" C4 G A 32 " ideal model delta sigma weight residual 1.375 1.362 0.013 8.00e-03 1.56e+04 2.66e+00 bond pdb=" N9 G A 227 " pdb=" C4 G A 227 " ideal model delta sigma weight residual 1.375 1.387 -0.012 8.00e-03 1.56e+04 2.39e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 15495 1.70 - 3.40: 1394 3.40 - 5.10: 49 5.10 - 6.80: 3 6.80 - 8.50: 3 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 121.90 117.61 4.29 7.00e-01 2.04e+00 3.75e+01 angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 118.20 3.70 7.00e-01 2.04e+00 2.80e+01 angle pdb=" O2 C A 386 " pdb=" C2 C A 386 " pdb=" N3 C A 386 " ideal model delta sigma weight residual 121.90 118.21 3.69 7.00e-01 2.04e+00 2.78e+01 angle pdb=" C2 C A 378 " pdb=" N1 C A 378 " pdb=" C6 C A 378 " ideal model delta sigma weight residual 120.30 118.34 1.96 4.00e-01 6.25e+00 2.40e+01 angle pdb=" N1 C A 366 " pdb=" C2 C A 366 " pdb=" O2 C A 366 " ideal model delta sigma weight residual 118.90 121.66 -2.76 6.00e-01 2.78e+00 2.11e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.76: 5871 32.76 - 65.52: 1103 65.52 - 98.28: 134 98.28 - 131.04: 6 131.04 - 163.80: 2 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual 200.00 40.63 159.37 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U A 34 " pdb=" C1' U A 34 " pdb=" N1 U A 34 " pdb=" C2 U A 34 " ideal model delta sinusoidal sigma weight residual -160.00 -83.09 -76.91 1 1.50e+01 4.44e-03 3.30e+01 dihedral pdb=" O4' A A 231 " pdb=" C1' A A 231 " pdb=" N9 A A 231 " pdb=" C4 A A 231 " ideal model delta sinusoidal sigma weight residual -106.00 -178.34 72.34 1 1.70e+01 3.46e-03 2.31e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1569 0.045 - 0.090: 217 0.090 - 0.135: 312 0.135 - 0.179: 120 0.179 - 0.224: 3 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C1' G A 358 " pdb=" O4' G A 358 " pdb=" C2' G A 358 " pdb=" N9 G A 358 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1' A A 332 " pdb=" O4' A A 332 " pdb=" C2' A A 332 " pdb=" N9 A A 332 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.01e-01 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 2.29 0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 262 " -0.034 2.00e-02 2.50e+03 1.65e-02 7.51e+00 pdb=" N9 A A 262 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A A 262 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A 262 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 262 " -0.010 2.00e-02 2.50e+03 pdb=" C6 A A 262 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A A 262 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A A 262 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 262 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 262 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A 262 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 261 " -0.035 2.00e-02 2.50e+03 1.62e-02 7.24e+00 pdb=" N9 A A 261 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A A 261 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A A 261 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 261 " -0.006 2.00e-02 2.50e+03 pdb=" C6 A A 261 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A 261 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 261 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A A 261 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 261 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A A 261 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.036 2.00e-02 2.50e+03 1.54e-02 7.10e+00 pdb=" N9 G A 298 " -0.036 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 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.004 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 23 2.51 - 3.11: 6709 3.11 - 3.70: 21555 3.70 - 4.30: 28073 4.30 - 4.90: 35425 Nonbonded interactions: 91785 Sorted by model distance: nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 510 " model vdw 1.910 2.170 nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 507 " model vdw 1.933 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 510 " model vdw 1.945 2.170 nonbonded pdb=" OP2 G A 288 " pdb="MG MG A 517 " model vdw 1.983 2.170 nonbonded pdb=" OP2 G A 14 " pdb="MG MG A 505 " model vdw 1.983 2.170 ... (remaining 91780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.480 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 0.032 11000 Z= 0.300 Angle : 0.853 8.502 16944 Z= 0.748 Chirality : 0.063 0.224 2221 Planarity : 0.004 0.020 581 Dihedral : 25.287 163.795 6900 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 3.03 % Allowed : 30.30 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.84), residues: 114 helix: 1.10 (0.77), residues: 53 sheet: -0.19 (0.84), residues: 26 loop : -2.55 (1.20), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.007 0.001 TYR B 31 PHE 0.011 0.001 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.30 (11000) covalent geometry : angle 0.85300 / 0.75 (16944) hydrogen bonds : bond 0.09649 / 9.19 ( 411) hydrogen bonds : angle 3.74976 / 4.53 ( 764) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.146 Fit side-chains REVERT: B 59 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8341 (ttp80) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.0930 time to fit residues: 3.8167 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 102 ILE 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: 5.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 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 = 0.3675 r_free = 0.3675 target = 0.063734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.038519 restraints weight = 63112.762| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.56 r_work: 0.2639 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 11000 Z= 0.548 Angle : 1.075 15.092 16944 Z= 0.532 Chirality : 0.075 0.372 2221 Planarity : 0.007 0.028 581 Dihedral : 25.543 165.444 6649 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 32.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 9.09 % Allowed : 23.23 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.78), residues: 114 helix: -0.34 (0.67), residues: 55 sheet: -2.44 (0.66), residues: 26 loop : -2.05 (1.37), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.019 0.004 TYR B 31 PHE 0.015 0.003 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.55 (11000) covalent geometry : angle 1.07487 / 0.53 (16944) hydrogen bonds : bond 0.14419 / 15.39 ( 411) hydrogen bonds : angle 3.32137 / 4.25 ( 764) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.088 Fit side-chains REVERT: B 92 MET cc_start: 0.9081 (pmm) cc_final: 0.8859 (pmm) REVERT: B 99 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8511 (mmmm) outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.0907 time to fit residues: 4.6304 Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 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 = 0.3667 r_free = 0.3667 target = 0.063303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038018 restraints weight = 63539.094| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.33 r_work: 0.2628 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 11000 Z= 0.474 Angle : 0.956 15.005 16944 Z= 0.487 Chirality : 0.064 0.376 2221 Planarity : 0.006 0.030 581 Dihedral : 25.877 162.497 6649 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 30.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 11.11 % Allowed : 23.23 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.81), residues: 114 helix: -0.29 (0.67), residues: 55 sheet: -2.73 (0.80), residues: 26 loop : -1.81 (1.36), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.017 0.003 TYR B 5 PHE 0.018 0.004 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.47 (11000) covalent geometry : angle 0.95629 / 0.49 (16944) hydrogen bonds : bond 0.13033 / 13.83 ( 411) hydrogen bonds : angle 3.22152 / 4.06 ( 764) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.135 Fit side-chains REVERT: B 99 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8570 (mmmm) outliers start: 11 outliers final: 7 residues processed: 36 average time/residue: 0.0850 time to fit residues: 4.4830 Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 30.0000 chunk 36 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.062822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037605 restraints weight = 64342.206| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.42 r_work: 0.2615 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3533 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= 0.488 Angle : 0.989 16.563 16944 Z= 0.501 Chirality : 0.068 0.401 2221 Planarity : 0.006 0.029 581 Dihedral : 25.980 160.639 6648 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 32.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 14.14 % Allowed : 22.22 % 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: -2.29 (0.80), residues: 114 helix: -0.43 (0.68), residues: 54 sheet: -2.60 (0.91), residues: 25 loop : -2.11 (1.25), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.014 0.002 TYR B 5 PHE 0.018 0.003 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.49 (11000) covalent geometry : angle 0.98893 / 0.50 (16944) hydrogen bonds : bond 0.14130 / 14.61 ( 411) hydrogen bonds : angle 3.30206 / 4.22 ( 764) *********************** 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 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.085 Fit side-chains REVERT: B 12 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8604 (mt-10) REVERT: B 27 GLN cc_start: 0.8401 (pt0) cc_final: 0.8072 (pt0) REVERT: B 40 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8027 (p90) outliers start: 14 outliers final: 8 residues processed: 36 average time/residue: 0.0706 time to fit residues: 3.6655 Evaluate side-chains 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.063085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.038436 restraints weight = 63322.377| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.85 r_work: 0.2642 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11000 Z= 0.352 Angle : 0.787 12.879 16944 Z= 0.423 Chirality : 0.055 0.336 2221 Planarity : 0.006 0.024 581 Dihedral : 25.975 159.097 6648 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 11.11 % Allowed : 23.23 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.82), residues: 114 helix: 0.04 (0.69), residues: 54 sheet: -2.23 (0.96), residues: 25 loop : -2.04 (1.26), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.014 0.002 TYR B 5 PHE 0.018 0.003 PHE B 68 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.35 (11000) covalent geometry : angle 0.78704 / 0.42 (16944) hydrogen bonds : bond 0.11794 / 12.07 ( 411) hydrogen bonds : angle 3.10152 / 4.05 ( 764) *********************** 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 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.173 Fit side-chains REVERT: B 12 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8566 (mt-10) REVERT: B 26 ARG cc_start: 0.8735 (mpt-90) cc_final: 0.8261 (mpt180) REVERT: B 40 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7935 (p90) outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 0.0766 time to fit residues: 3.8429 Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.063134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.038068 restraints weight = 63687.298| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.69 r_work: 0.2633 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.3655 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= 0.324 Angle : 0.755 11.704 16944 Z= 0.408 Chirality : 0.053 0.308 2221 Planarity : 0.005 0.025 581 Dihedral : 25.886 158.383 6648 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 8.08 % Allowed : 23.23 % Favored : 68.69 % 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: -1.78 (0.81), residues: 114 helix: 0.55 (0.73), residues: 48 sheet: -2.04 (0.95), residues: 25 loop : -2.66 (1.09), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 59 TYR 0.012 0.002 TYR B 5 PHE 0.019 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.32 (11000) covalent geometry : angle 0.75467 / 0.41 (16944) hydrogen bonds : bond 0.11193 / 11.32 ( 411) hydrogen bonds : angle 3.02948 / 3.83 ( 764) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.086 Fit side-chains REVERT: B 12 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8566 (mt-10) REVERT: B 26 ARG cc_start: 0.8731 (mpt-90) cc_final: 0.8286 (mpt180) REVERT: B 68 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8192 (t80) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.0716 time to fit residues: 3.4709 Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 overall best weight: 4.7790 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.063045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037889 restraints weight = 63748.449| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.70 r_work: 0.2643 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11000 Z= 0.337 Angle : 0.760 12.073 16944 Z= 0.409 Chirality : 0.054 0.313 2221 Planarity : 0.006 0.024 581 Dihedral : 25.895 157.641 6647 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % Favored : 66.67 % 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: -1.95 (0.81), residues: 114 helix: -0.23 (0.69), residues: 54 sheet: -2.20 (0.95), residues: 25 loop : -2.01 (1.23), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.013 0.002 TYR B 5 PHE 0.014 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.34 (11000) covalent geometry : angle 0.75953 / 0.41 (16944) hydrogen bonds : bond 0.11172 / 11.35 ( 411) hydrogen bonds : angle 3.09652 / 3.94 ( 764) *********************** 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 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.149 Fit side-chains REVERT: B 12 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8579 (mt-10) REVERT: B 26 ARG cc_start: 0.8718 (mpt-90) cc_final: 0.8262 (mpt180) REVERT: B 40 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.7950 (p90) REVERT: B 68 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8127 (t80) outliers start: 9 outliers final: 5 residues processed: 33 average time/residue: 0.0966 time to fit residues: 4.6012 Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.063422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038162 restraints weight = 62948.097| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.50 r_work: 0.2657 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11000 Z= 0.242 Angle : 0.655 9.829 16944 Z= 0.369 Chirality : 0.047 0.282 2221 Planarity : 0.005 0.026 581 Dihedral : 25.837 157.136 6647 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 7.07 % Allowed : 27.27 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.82), residues: 114 helix: 0.04 (0.73), residues: 54 sheet: -1.87 (0.96), residues: 25 loop : -2.00 (1.22), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.010 0.002 TYR B 5 PHE 0.017 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.24 (11000) covalent geometry : angle 0.65495 / 0.37 (16944) hydrogen bonds : bond 0.09965 / 10.04 ( 411) hydrogen bonds : angle 2.98011 / 3.70 ( 764) *********************** 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 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.139 Fit side-chains REVERT: B 12 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8557 (mt-10) REVERT: B 26 ARG cc_start: 0.8637 (mpt-90) cc_final: 0.8186 (mpt180) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.0955 time to fit residues: 4.8461 Evaluate side-chains 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.062072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037261 restraints weight = 64179.243| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.59 r_work: 0.2590 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 11000 Z= 0.576 Angle : 1.078 18.095 16944 Z= 0.531 Chirality : 0.074 0.393 2221 Planarity : 0.007 0.069 581 Dihedral : 25.962 156.969 6647 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 36.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 8.08 % Allowed : 25.25 % Favored : 66.67 % 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: -2.33 (0.80), residues: 114 helix: -0.59 (0.70), residues: 54 sheet: -2.28 (0.96), residues: 25 loop : -2.20 (1.17), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 59 TYR 0.017 0.003 TYR B 5 PHE 0.016 0.003 PHE B 68 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.58 (11000) covalent geometry : angle 1.07813 / 0.53 (16944) hydrogen bonds : bond 0.14377 / 14.85 ( 411) hydrogen bonds : angle 3.42980 / 4.37 ( 764) *********************** 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 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.137 Fit side-chains REVERT: B 26 ARG cc_start: 0.8764 (mpt-90) cc_final: 0.8278 (mpt180) REVERT: B 40 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8030 (p90) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.0969 time to fit residues: 4.3723 Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.062541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037748 restraints weight = 63628.459| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.91 r_work: 0.2628 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11000 Z= 0.405 Angle : 0.870 13.709 16944 Z= 0.453 Chirality : 0.061 0.349 2221 Planarity : 0.006 0.057 581 Dihedral : 25.992 155.712 6647 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 29.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 7.07 % Allowed : 28.28 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.82), residues: 114 helix: -0.36 (0.74), residues: 54 sheet: -2.31 (0.93), residues: 25 loop : -2.09 (1.19), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.015 0.002 TYR B 5 PHE 0.016 0.003 PHE B 68 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.40 (11000) covalent geometry : angle 0.86989 / 0.45 (16944) hydrogen bonds : bond 0.12190 / 12.58 ( 411) hydrogen bonds : angle 3.26517 / 4.14 ( 764) ********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.152 Fit side-chains REVERT: B 26 ARG cc_start: 0.8716 (mpt-90) cc_final: 0.8225 (mpt180) REVERT: B 40 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7980 (p90) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.1039 time to fit residues: 4.5780 Evaluate side-chains 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.063355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038124 restraints weight = 63124.752| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.46 r_work: 0.2662 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11000 Z= 0.220 Angle : 0.626 9.575 16944 Z= 0.362 Chirality : 0.044 0.287 2221 Planarity : 0.005 0.054 581 Dihedral : 25.877 157.629 6647 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 5.05 % Allowed : 30.30 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.84), residues: 114 helix: 0.00 (0.76), residues: 54 sheet: -1.89 (0.93), residues: 25 loop : -2.00 (1.24), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 59 TYR 0.010 0.002 TYR B 5 PHE 0.014 0.002 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.22 (11000) covalent geometry : angle 0.62611 / 0.36 (16944) hydrogen bonds : bond 0.09765 / 9.92 ( 411) hydrogen bonds : angle 2.97699 / 3.72 ( 764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.01 seconds wall clock time: 52 minutes 51.41 seconds (3171.41 seconds total)