Starting phenix.real_space_refine on Wed Aug 5 13:23:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zie_74271/08_2026/9zie_74271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zie_74271/08_2026/9zie_74271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zie_74271/08_2026/9zie_74271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zie_74271/08_2026/9zie_74271.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zie_74271/08_2026/9zie_74271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zie_74271/08_2026/9zie_74271.map" } resolution = 3.16 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 36 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9946 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': 29, 'rna2p_pyr': 20, 'rna3p_pur': 214, 'rna3p_pyr': 154} Link IDs: {'rna2p': 49, 'rna3p': 367} 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Unusual residues: {' MG': 36} Classifications: {'undetermined': 36, 'water': 1} Link IDs: {None: 36} Time building chain proxies: 2.22, per 1000 atoms: 0.22 Number of scatterers: 9946 At special positions: 0 Unit cell: (121.512, 170.556, 144.936, 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 36 11.99 O 3052 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: 0.78 Conformation dependent library (CDL) restraints added in 68.8 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 44.8% alpha, 15.5% beta 140 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.509A pdb=" N ARG B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.737A pdb=" N GLU B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.644A pdb=" N PHE B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 42 " --> pdb=" O LYS B 79 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.09 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: 1215 1.33 - 1.45: 5197 1.45 - 1.57: 3749 1.57 - 1.69: 834 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 189 " pdb=" C4 A A 189 " ideal model delta sigma weight residual 1.374 1.385 -0.011 6.00e-03 2.78e+04 3.66e+00 bond pdb=" N9 G A 372 " pdb=" C4 G A 372 " ideal model delta sigma weight residual 1.375 1.390 -0.015 8.00e-03 1.56e+04 3.39e+00 bond pdb=" CB GLU B 73 " pdb=" CG GLU B 73 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.59e+00 bond pdb=" C3' C A 414 " pdb=" O3' C A 414 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.20e-02 6.94e+03 2.54e+00 bond pdb=" C3' U A 33 " pdb=" O3' U A 33 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.20e-02 6.94e+03 2.45e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15378 1.55 - 3.10: 1463 3.10 - 4.65: 84 4.65 - 6.20: 13 6.20 - 7.75: 6 Bond angle restraints: 16944 Sorted by residual: angle pdb=" C3' C A 414 " pdb=" O3' C A 414 " pdb=" P G A 415 " ideal model delta sigma weight residual 119.70 126.17 -6.47 1.20e+00 6.94e-01 2.91e+01 angle pdb=" C3' U A 33 " pdb=" O3' U A 33 " pdb=" P U A 34 " ideal model delta sigma weight residual 119.70 125.77 -6.07 1.20e+00 6.94e-01 2.56e+01 angle pdb=" N1 C A 182 " pdb=" C2 C A 182 " pdb=" O2 C A 182 " ideal model delta sigma weight residual 118.90 121.67 -2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sigma weight residual 117.70 123.13 -5.43 1.20e+00 6.94e-01 2.05e+01 angle pdb=" O2 C A 182 " pdb=" C2 C A 182 " pdb=" N3 C A 182 " ideal model delta sigma weight residual 121.90 118.81 3.09 7.00e-01 2.04e+00 1.94e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 5973 35.84 - 71.68: 997 71.68 - 107.53: 133 107.53 - 143.37: 6 143.37 - 179.21: 7 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual -160.00 11.14 -171.14 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U A 371 " pdb=" C1' U A 371 " pdb=" N1 U A 371 " pdb=" C2 U A 371 " ideal model delta sinusoidal sigma weight residual -160.00 -64.50 -95.50 1 1.50e+01 4.44e-03 4.68e+01 dihedral pdb=" O4' C A 318 " pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sinusoidal sigma weight residual -128.00 -50.13 -77.87 1 1.70e+01 3.46e-03 2.62e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1571 0.046 - 0.092: 218 0.092 - 0.137: 356 0.137 - 0.183: 68 0.183 - 0.229: 8 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C3' U A 185 " pdb=" C4' U A 185 " pdb=" O3' U A 185 " pdb=" C2' U A 185 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1' A A 50 " pdb=" O4' A A 50 " pdb=" C2' A A 50 " pdb=" N9 A A 50 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' A A 146 " pdb=" C4' A A 146 " pdb=" O3' A A 146 " pdb=" C2' A A 146 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 200 " -0.041 2.00e-02 2.50e+03 1.79e-02 9.59e+00 pdb=" N9 G A 200 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G A 200 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 200 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 200 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G A 200 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G A 200 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G A 200 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 200 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G A 200 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 200 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A 200 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 187 " -0.038 2.00e-02 2.50e+03 1.82e-02 9.06e+00 pdb=" N9 A A 187 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A A 187 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 187 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 187 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 187 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A 187 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 187 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 187 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A A 187 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A 187 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.033 2.00e-02 2.50e+03 1.46e-02 6.43e+00 pdb=" N9 G A 298 " -0.036 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.003 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 35 2.49 - 3.09: 6389 3.09 - 3.69: 21144 3.69 - 4.30: 28403 4.30 - 4.90: 35788 Nonbonded interactions: 91759 Sorted by model distance: nonbonded pdb=" OP1 A A 50 " pdb="MG MG A 505 " model vdw 1.884 2.170 nonbonded pdb="MG MG A 505 " pdb=" O HOH A 601 " model vdw 1.917 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 512 " model vdw 1.963 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 512 " model vdw 1.966 2.170 nonbonded pdb=" N2 G A 1 " pdb=" O2 C A 414 " model vdw 1.997 2.496 ... (remaining 91754 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: 11.100 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 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 0.048 11000 Z= 0.281 Angle : 0.862 7.747 16944 Z= 0.720 Chirality : 0.064 0.229 2221 Planarity : 0.004 0.039 581 Dihedral : 25.836 179.211 6900 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.26 % Favored : 93.86 % Rotamer: Outliers : 2.02 % Allowed : 28.28 % Favored : 69.70 % 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: 0.79 (0.86), residues: 114 helix: 2.05 (0.82), residues: 46 sheet: 1.59 (1.17), residues: 26 loop : -2.08 (0.91), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 26 TYR 0.023 0.002 TYR B 5 PHE 0.006 0.001 PHE B 17 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.28 (11000) covalent geometry : angle 0.86159 / 0.72 (16944) hydrogen bonds : bond 0.10143 / 10.00 ( 403) hydrogen bonds : angle 4.80033 / 5.22 ( 744) *********************** 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.119 Fit side-chains REVERT: B 12 GLU cc_start: 0.9094 (mp0) cc_final: 0.8891 (mp0) REVERT: B 14 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8776 (mp10) REVERT: B 74 GLU cc_start: 0.7834 (tp30) cc_final: 0.7483 (tp30) REVERT: B 103 HIS cc_start: 0.8556 (t-170) cc_final: 0.8282 (t-90) REVERT: B 111 LEU cc_start: 0.8453 (mp) cc_final: 0.8124 (mt) outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 0.0891 time to fit residues: 4.1622 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 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 = 0.3961 r_free = 0.3961 target = 0.084260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047681 restraints weight = 58755.060| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.19 r_work: 0.2611 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 11000 Z= 0.514 Angle : 0.955 9.976 16944 Z= 0.479 Chirality : 0.069 0.427 2221 Planarity : 0.006 0.028 581 Dihedral : 26.077 177.681 6649 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 23.23 % Favored : 70.71 % 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: -1.14 (0.75), residues: 114 helix: 0.56 (0.68), residues: 46 sheet: -0.16 (1.11), residues: 28 loop : -2.79 (0.81), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.007 0.002 TYR B 31 PHE 0.018 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.51 (11000) covalent geometry : angle 0.95474 / 0.48 (16944) hydrogen bonds : bond 0.13119 / 13.74 ( 403) hydrogen bonds : angle 3.13280 / 3.51 ( 744) *********************** 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: 6 poor density : 28 time to evaluate : 0.144 Fit side-chains REVERT: B 74 GLU cc_start: 0.8610 (tp30) cc_final: 0.8076 (tp30) REVERT: B 86 ARG cc_start: 0.8688 (mtm180) cc_final: 0.8486 (mtm180) REVERT: B 103 HIS cc_start: 0.8700 (t-170) cc_final: 0.8349 (t-170) outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.0841 time to fit residues: 4.1317 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 50.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.084079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046775 restraints weight = 59284.470| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.50 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2128 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= 0.365 Angle : 0.788 8.699 16944 Z= 0.413 Chirality : 0.055 0.420 2221 Planarity : 0.006 0.028 581 Dihedral : 26.303 177.384 6647 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.04 % Allowed : 29.29 % 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: -1.51 (0.74), residues: 114 helix: 0.81 (0.71), residues: 46 sheet: -0.96 (0.97), residues: 28 loop : -3.25 (0.81), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 26 TYR 0.011 0.002 TYR B 94 PHE 0.019 0.005 PHE B 41 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.37 (11000) covalent geometry : angle 0.78764 / 0.41 (16944) hydrogen bonds : bond 0.11134 / 11.80 ( 403) hydrogen bonds : angle 3.04350 / 3.47 ( 744) *********************** 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.109 Fit side-chains REVERT: B 14 GLN cc_start: 0.9036 (mp10) cc_final: 0.8618 (mm-40) REVERT: B 18 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8628 (mm-40) REVERT: B 74 GLU cc_start: 0.8311 (tp30) cc_final: 0.8034 (tp30) REVERT: B 103 HIS cc_start: 0.8637 (t-170) cc_final: 0.8321 (t-170) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.0947 time to fit residues: 4.2470 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 41 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.083350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046102 restraints weight = 59406.567| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.01 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2741 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= 0.424 Angle : 0.870 9.616 16944 Z= 0.448 Chirality : 0.062 0.418 2221 Planarity : 0.006 0.025 581 Dihedral : 26.404 177.884 6645 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 26.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 26.26 % 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: -1.70 (0.75), residues: 114 helix: 0.33 (0.70), residues: 47 sheet: -0.44 (1.07), residues: 26 loop : -3.39 (0.82), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 26 TYR 0.015 0.002 TYR B 94 PHE 0.017 0.004 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.42 (11000) covalent geometry : angle 0.87036 / 0.45 (16944) hydrogen bonds : bond 0.12791 / 13.59 ( 403) hydrogen bonds : angle 3.18289 / 3.62 ( 744) *********************** 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.137 Fit side-chains REVERT: B 1 MET cc_start: 0.8737 (tpp) cc_final: 0.8284 (mmm) REVERT: B 14 GLN cc_start: 0.8970 (mp10) cc_final: 0.8571 (mm-40) REVERT: B 74 GLU cc_start: 0.8449 (tp30) cc_final: 0.8011 (tp30) REVERT: B 103 HIS cc_start: 0.8634 (t-170) cc_final: 0.8288 (t-170) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 0.0782 time to fit residues: 3.8256 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 22 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 overall best weight: 3.7384 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.083869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047021 restraints weight = 58523.242| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.23 r_work: 0.2623 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11000 Z= 0.279 Angle : 0.694 9.019 16944 Z= 0.380 Chirality : 0.050 0.410 2221 Planarity : 0.005 0.025 581 Dihedral : 26.385 177.542 6645 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.04 % Allowed : 28.28 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.78), residues: 114 helix: 1.02 (0.75), residues: 47 sheet: -0.18 (1.08), residues: 26 loop : -3.09 (0.82), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 26 TYR 0.012 0.001 TYR B 94 PHE 0.016 0.003 PHE B 13 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.28 (11000) covalent geometry : angle 0.69406 / 0.38 (16944) hydrogen bonds : bond 0.10610 / 11.23 ( 403) hydrogen bonds : angle 2.95792 / 3.30 ( 744) *********************** 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.142 Fit side-chains REVERT: B 14 GLN cc_start: 0.9004 (mp10) cc_final: 0.8620 (mm-40) REVERT: B 27 GLN cc_start: 0.8833 (mp10) cc_final: 0.8245 (mp10) REVERT: B 74 GLU cc_start: 0.8763 (tp30) cc_final: 0.8270 (tp30) REVERT: B 86 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7523 (mtm180) REVERT: B 103 HIS cc_start: 0.8708 (t-170) cc_final: 0.8404 (t-170) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.0901 time to fit residues: 4.2584 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 86 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.083564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.046643 restraints weight = 58426.248| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.37 r_work: 0.2641 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11000 Z= 0.322 Angle : 0.736 9.382 16944 Z= 0.394 Chirality : 0.052 0.411 2221 Planarity : 0.005 0.026 581 Dihedral : 26.343 178.098 6645 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.03 % Allowed : 28.28 % 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: -1.08 (0.76), residues: 114 helix: 0.97 (0.74), residues: 46 sheet: -0.21 (1.05), residues: 26 loop : -3.08 (0.79), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 26 TYR 0.011 0.001 TYR B 94 PHE 0.015 0.003 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.32 (11000) covalent geometry : angle 0.73557 / 0.39 (16944) hydrogen bonds : bond 0.10986 / 11.47 ( 403) hydrogen bonds : angle 3.01137 / 3.34 ( 744) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.160 Fit side-chains REVERT: B 14 GLN cc_start: 0.9016 (mp10) cc_final: 0.8622 (mm-40) REVERT: B 27 GLN cc_start: 0.8957 (mp10) cc_final: 0.8346 (mp10) REVERT: B 74 GLU cc_start: 0.8851 (tp30) cc_final: 0.8409 (tp30) REVERT: B 86 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7522 (mtm180) REVERT: B 103 HIS cc_start: 0.8710 (t-170) cc_final: 0.8384 (t-170) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.0871 time to fit residues: 3.9393 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 86 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.082837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047606 restraints weight = 58825.064| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.33 r_work: 0.2575 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 11000 Z= 0.449 Angle : 0.928 10.802 16944 Z= 0.474 Chirality : 0.065 0.432 2221 Planarity : 0.006 0.027 581 Dihedral : 26.511 178.023 6645 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 29.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.03 % Allowed : 28.28 % 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 (0.74), residues: 114 helix: 0.38 (0.71), residues: 46 sheet: -0.90 (1.06), residues: 27 loop : -3.21 (0.76), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.010 0.002 TYR B 94 PHE 0.015 0.003 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.45 (11000) covalent geometry : angle 0.92804 / 0.47 (16944) hydrogen bonds : bond 0.12856 / 13.26 ( 403) hydrogen bonds : angle 3.25365 / 3.65 ( 744) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.113 Fit side-chains REVERT: B 14 GLN cc_start: 0.9019 (mp10) cc_final: 0.8654 (mm-40) REVERT: B 27 GLN cc_start: 0.8991 (mp10) cc_final: 0.8713 (mp10) REVERT: B 74 GLU cc_start: 0.8970 (tp30) cc_final: 0.8528 (tp30) REVERT: B 86 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7541 (mtm180) REVERT: B 103 HIS cc_start: 0.8744 (t-170) cc_final: 0.8413 (t-170) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.0725 time to fit residues: 3.2023 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 86 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 7.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.082145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045408 restraints weight = 59046.590| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.02 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 11000 Z= 0.557 Angle : 1.112 12.226 16944 Z= 0.552 Chirality : 0.077 0.455 2221 Planarity : 0.007 0.031 581 Dihedral : 26.845 176.579 6645 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 36.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 6.06 % Allowed : 28.28 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.69), residues: 114 helix: -0.74 (0.68), residues: 46 sheet: -1.21 (1.04), residues: 27 loop : -3.99 (0.68), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.007 0.002 TYR B 5 PHE 0.020 0.004 PHE B 13 HIS 0.005 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.56 (11000) covalent geometry : angle 1.11241 / 0.55 (16944) hydrogen bonds : bond 0.14798 / 15.08 ( 403) hydrogen bonds : angle 3.51702 / 3.98 ( 744) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.091 Fit side-chains REVERT: B 12 GLU cc_start: 0.9259 (mp0) cc_final: 0.9003 (mp0) REVERT: B 14 GLN cc_start: 0.9010 (mp10) cc_final: 0.8698 (mm-40) REVERT: B 18 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8762 (mm-40) REVERT: B 74 GLU cc_start: 0.8867 (tp30) cc_final: 0.8347 (tp30) REVERT: B 86 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7437 (mtm180) REVERT: B 103 HIS cc_start: 0.8634 (t-170) cc_final: 0.8399 (t-170) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.0684 time to fit residues: 2.9535 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 50.0000 chunk 6 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.082701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046942 restraints weight = 57791.770| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.79 r_work: 0.2585 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11000 Z= 0.389 Angle : 0.859 10.646 16944 Z= 0.454 Chirality : 0.060 0.422 2221 Planarity : 0.006 0.028 581 Dihedral : 26.772 174.053 6645 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 29.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.04 % Allowed : 32.32 % 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: -2.39 (0.72), residues: 114 helix: 0.03 (0.71), residues: 46 sheet: -1.02 (1.03), residues: 27 loop : -3.93 (0.67), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 6 TYR 0.005 0.001 TYR B 94 PHE 0.014 0.003 PHE B 13 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.39 (11000) covalent geometry : angle 0.85900 / 0.45 (16944) hydrogen bonds : bond 0.11991 / 12.26 ( 403) hydrogen bonds : angle 3.23514 / 3.60 ( 744) *********************** 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.104 Fit side-chains REVERT: B 14 GLN cc_start: 0.8979 (mp10) cc_final: 0.8713 (mm-40) REVERT: B 27 GLN cc_start: 0.8976 (mp10) cc_final: 0.8682 (mp10) REVERT: B 74 GLU cc_start: 0.9015 (tp30) cc_final: 0.8582 (tp30) REVERT: B 86 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7519 (mtm180) REVERT: B 96 GLU cc_start: 0.8835 (pm20) cc_final: 0.8594 (pm20) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.0932 time to fit residues: 4.2735 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 86 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.082701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045982 restraints weight = 57727.558| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.48 r_work: 0.2601 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11000 Z= 0.388 Angle : 0.843 9.955 16944 Z= 0.444 Chirality : 0.059 0.418 2221 Planarity : 0.006 0.066 581 Dihedral : 26.654 172.624 6645 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 29.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 30.30 % 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: -2.10 (0.72), residues: 114 helix: 0.37 (0.72), residues: 46 sheet: -1.03 (0.97), residues: 27 loop : -3.79 (0.70), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.006 0.001 TYR B 94 PHE 0.018 0.003 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.39 (11000) covalent geometry : angle 0.84292 / 0.44 (16944) hydrogen bonds : bond 0.11511 / 11.53 ( 403) hydrogen bonds : angle 3.18470 / 3.50 ( 744) ********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.098 Fit side-chains REVERT: B 14 GLN cc_start: 0.9029 (mp10) cc_final: 0.8766 (mm-40) REVERT: B 27 GLN cc_start: 0.9047 (mp10) cc_final: 0.8797 (mp10) REVERT: B 74 GLU cc_start: 0.9018 (tp30) cc_final: 0.8546 (tp30) REVERT: B 86 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7495 (mtm180) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0823 time to fit residues: 3.5288 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 86 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.082739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046268 restraints weight = 58665.275| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.47 r_work: 0.2597 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 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 : 0.007 0.227 11000 Z= 0.418 Angle : 1.030 59.098 16944 Z= 0.579 Chirality : 0.071 1.888 2221 Planarity : 0.006 0.059 581 Dihedral : 26.655 172.622 6645 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 29.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.65 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 29.29 % Favored : 66.67 % Cbeta Deviations : 0.93 % 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 (0.72), residues: 114 helix: 0.38 (0.72), residues: 46 sheet: -1.15 (0.95), residues: 27 loop : -3.79 (0.70), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.004 0.001 TYR B 5 PHE 0.017 0.003 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.42 (11000) covalent geometry : angle 1.02976 / 0.58 (16944) hydrogen bonds : bond 0.11498 / 11.52 ( 403) hydrogen bonds : angle 3.22010 / 3.59 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4105.04 seconds wall clock time: 70 minutes 34.78 seconds (4234.78 seconds total)