Starting phenix.real_space_refine on Wed Aug 5 23:15:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owx_70947/08_2026/9owx_70947_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owx_70947/08_2026/9owx_70947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9owx_70947/08_2026/9owx_70947_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owx_70947/08_2026/9owx_70947_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9owx_70947/08_2026/9owx_70947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owx_70947/08_2026/9owx_70947.map" } resolution = 2.7 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 Ca 27 9.91 5 P 525 5.49 5 S 3 5.16 5 C 5626 2.51 5 N 2231 2.21 5 O 3817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 12229 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 26, 'rna2p_pyr': 15, 'rna3p_pur': 217, 'rna3p_pyr': 159} Link IDs: {'rna2p': 41, 'rna3p': 375} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2293 Classifications: {'RNA': 108} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 40, 'rna3p_pyr': 50} Link IDs: {'rna2p': 17, 'rna3p': 90} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Unusual residues: {' CA': 26} Classifications: {'undetermined': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.15 Number of scatterers: 12229 At special positions: 0 Unit cell: (126.49, 159.667, 129.6, 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) Ca 27 19.99 S 3 16.00 P 525 15.00 O 3817 8.00 N 2231 7.00 C 5626 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: 0.89 Conformation dependent library (CDL) restraints added in 164.9 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 44.0% alpha, 16.4% beta 183 base pairs and 313 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.526A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 6.090A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 467 hydrogen bonds 788 hydrogen bond angles 0 basepair planarities 183 basepair parallelities 313 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 2899 1.36 - 1.51: 7434 1.51 - 1.67: 3219 1.67 - 1.82: 5 1.82 - 1.98: 1 Bond restraints: 13558 Sorted by residual: bond pdb=" O3' U C 11 " pdb=" P U C 12 " ideal model delta sigma weight residual 1.607 1.979 -0.372 1.20e-02 6.94e+03 9.60e+02 bond pdb=" CA SER B 100 " pdb=" CB SER B 100 " ideal model delta sigma weight residual 1.529 1.422 0.107 1.55e-02 4.16e+03 4.74e+01 bond pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 1.522 1.457 0.064 1.37e-02 5.33e+03 2.19e+01 bond pdb=" CA ALA B 95 " pdb=" CB ALA B 95 " ideal model delta sigma weight residual 1.532 1.460 0.072 1.65e-02 3.67e+03 1.89e+01 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.14e+01 ... (remaining 13553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 19334 3.01 - 6.02: 1410 6.02 - 9.03: 173 9.03 - 12.04: 9 12.04 - 15.04: 2 Bond angle restraints: 20928 Sorted by residual: angle pdb=" O3' U C 11 " pdb=" P U C 12 " pdb=" O5' U C 12 " ideal model delta sigma weight residual 104.00 119.04 -15.04 1.90e+00 2.77e-01 6.27e+01 angle pdb=" C3' A A 377 " pdb=" C2' A A 377 " pdb=" C1' A A 377 " ideal model delta sigma weight residual 101.30 96.44 4.86 7.00e-01 2.04e+00 4.83e+01 angle pdb=" C4' A A 377 " pdb=" C3' A A 377 " pdb=" C2' A A 377 " ideal model delta sigma weight residual 102.60 96.09 6.51 1.00e+00 1.00e+00 4.23e+01 angle pdb=" C4' U A 67 " pdb=" O4' U A 67 " pdb=" C1' U A 67 " ideal model delta sigma weight residual 109.70 105.26 4.44 7.00e-01 2.04e+00 4.02e+01 angle pdb=" C3' C C 69 " pdb=" C2' C C 69 " pdb=" C1' C C 69 " ideal model delta sigma weight residual 101.30 96.90 4.40 7.00e-01 2.04e+00 3.94e+01 ... (remaining 20923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 7141 35.93 - 71.87: 1496 71.87 - 107.80: 186 107.80 - 143.74: 7 143.74 - 179.67: 9 Dihedral angle restraints: 8839 sinusoidal: 8502 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 16.24 -176.24 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U C 59 " pdb=" C1' U C 59 " pdb=" N1 U C 59 " pdb=" C2 U C 59 " ideal model delta sinusoidal sigma weight residual 232.00 52.33 179.67 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C C -4 " pdb=" C1' C C -4 " pdb=" N1 C C -4 " pdb=" C2 C C -4 " ideal model delta sinusoidal sigma weight residual 232.00 57.16 174.84 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 8836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1913 0.125 - 0.249: 476 0.249 - 0.374: 143 0.374 - 0.499: 212 0.499 - 0.624: 17 Chirality restraints: 2761 Sorted by residual: chirality pdb=" P G A 268 " pdb=" OP1 G A 268 " pdb=" OP2 G A 268 " pdb=" O5' G A 268 " both_signs ideal model delta sigma weight residual True 2.41 -3.03 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" P G C -32 " pdb=" OP1 G C -32 " pdb=" OP2 G C -32 " pdb=" O5' G C -32 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" P C C 47 " pdb=" OP1 C C 47 " pdb=" OP2 C C 47 " pdb=" O5' C C 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.62e+00 ... (remaining 2758 not shown) Planarity restraints: 689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " 0.413 9.50e-02 1.11e+02 1.85e-01 2.10e+01 pdb=" NE ARG B 59 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 110 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C GLY B 110 " -0.070 2.00e-02 2.50e+03 pdb=" O GLY B 110 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU B 111 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 299 " 0.050 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" N9 G A 299 " -0.042 2.00e-02 2.50e+03 pdb=" C8 G A 299 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G A 299 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 299 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 299 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G A 299 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A 299 " 0.008 2.00e-02 2.50e+03 pdb=" C2 G A 299 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 299 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G A 299 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G A 299 " -0.010 2.00e-02 2.50e+03 ... (remaining 686 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.71: 7 1.71 - 2.51: 97 2.51 - 3.31: 13399 3.31 - 4.10: 47720 4.10 - 4.90: 60121 Warning: very small nonbonded interaction distances. Nonbonded interactions: 121344 Sorted by model distance: nonbonded pdb=" OP2 C A 160 " pdb=" C6 C A 160 " model vdw 0.915 3.340 nonbonded pdb=" OP2 U A 293 " pdb="CA CA A 521 " model vdw 1.038 2.510 nonbonded pdb=" OP2 A A 364 " pdb=" C8 G A 365 " model vdw 1.337 3.260 nonbonded pdb=" O3' A A 363 " pdb=" C8 A A 364 " model vdw 1.361 3.260 nonbonded pdb=" C3' A A 363 " pdb=" C8 A A 364 " model vdw 1.368 3.690 ... (remaining 121339 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: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.040 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 : 0.010 0.372 13558 Z= 0.776 Angle : 1.633 15.045 20928 Z= 0.979 Chirality : 0.166 0.624 2761 Planarity : 0.009 0.185 689 Dihedral : 28.084 179.673 8623 Min Nonbonded Distance : 0.915 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 1.75 % Allowed : 2.63 % Favored : 95.61 % 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: 0.71 (0.79), residues: 114 helix: 1.15 (0.85), residues: 47 sheet: 0.87 (0.82), residues: 29 loop : -0.62 (0.96), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.007 0.001 TYR B 94 PHE 0.004 0.001 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00994 / 0.78 (13558) covalent geometry : angle 1.63281 / 0.98 (20928) hydrogen bonds : bond 0.20255 / 20.62 ( 512) hydrogen bonds : angle 8.89478 / 11.23 ( 917) *********************** 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 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.151 Fit side-chains REVERT: B 3 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8720 (mtmm) REVERT: B 12 GLU cc_start: 0.8622 (mp0) cc_final: 0.8173 (mt-10) REVERT: B 15 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 21 VAL cc_start: 0.8588 (t) cc_final: 0.8308 (p) REVERT: B 40 TYR cc_start: 0.8545 (p90) cc_final: 0.8331 (p90) REVERT: B 71 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8057 (pp) outliers start: 9 outliers final: 1 residues processed: 34 average time/residue: 0.6993 time to fit residues: 25.4448 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 99 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 40.0000 chunk 61 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.092977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054574 restraints weight = 36517.843| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.32 r_work: 0.2877 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 13558 Z= 0.538 Angle : 0.985 13.057 20928 Z= 0.515 Chirality : 0.069 0.562 2761 Planarity : 0.008 0.036 689 Dihedral : 27.011 178.928 8378 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 16.16 % Allowed : 13.13 % 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: 0.72 (0.79), residues: 114 helix: 0.53 (0.72), residues: 48 sheet: 1.00 (0.89), residues: 29 loop : 0.22 (1.17), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG B 86 TYR 0.009 0.003 TYR B 5 PHE 0.018 0.005 PHE B 68 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.54 (13558) covalent geometry : angle 0.98548 / 0.51 (20928) hydrogen bonds : bond 0.12085 / 13.23 ( 512) hydrogen bonds : angle 2.94816 / 3.82 ( 917) *********************** 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: 16 poor density : 18 time to evaluate : 0.140 Fit side-chains REVERT: B 3 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8947 (mtmm) REVERT: B 12 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8747 (mt-10) outliers start: 16 outliers final: 7 residues processed: 29 average time/residue: 0.7184 time to fit residues: 22.2226 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 31 optimal weight: 10.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.091564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053297 restraints weight = 36887.641| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.31 r_work: 0.2845 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 13558 Z= 0.617 Angle : 1.007 14.272 20928 Z= 0.515 Chirality : 0.069 0.711 2761 Planarity : 0.008 0.039 689 Dihedral : 26.895 178.172 8378 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 12.12 % Allowed : 16.16 % Favored : 71.72 % 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: 0.01 (0.79), residues: 114 helix: -0.44 (0.68), residues: 47 sheet: 0.47 (0.81), residues: 29 loop : 0.61 (1.27), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 86 TYR 0.015 0.004 TYR B 94 PHE 0.020 0.006 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00960 / 0.62 (13558) covalent geometry : angle 1.00710 / 0.52 (20928) hydrogen bonds : bond 0.14093 / 15.26 ( 512) hydrogen bonds : angle 3.00984 / 3.77 ( 917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 16 time to evaluate : 0.155 Fit side-chains REVERT: B 38 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7993 (tt0) outliers start: 12 outliers final: 6 residues processed: 25 average time/residue: 0.8597 time to fit residues: 22.6871 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 99 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 25 optimal weight: 3.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.093485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.056649 restraints weight = 38755.915| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.08 r_work: 0.2970 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 13558 Z= 0.478 Angle : 0.824 13.194 20928 Z= 0.439 Chirality : 0.059 0.565 2761 Planarity : 0.007 0.034 689 Dihedral : 26.770 177.029 8374 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 10.10 % Allowed : 21.21 % 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: 0.67 (0.80), residues: 114 helix: 0.47 (0.74), residues: 48 sheet: 0.71 (0.84), residues: 29 loop : 0.49 (1.21), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 86 TYR 0.015 0.004 TYR B 94 PHE 0.017 0.004 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.48 (13558) covalent geometry : angle 0.82404 / 0.44 (20928) hydrogen bonds : bond 0.10676 / 11.71 ( 512) hydrogen bonds : angle 2.64784 / 3.32 ( 917) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.112 Fit side-chains REVERT: B 12 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8685 (mt-10) outliers start: 10 outliers final: 5 residues processed: 23 average time/residue: 0.8449 time to fit residues: 20.5405 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 74 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 4.4986 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.093211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056413 restraints weight = 38984.990| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.14 r_work: 0.2972 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 13558 Z= 0.472 Angle : 0.824 11.073 20928 Z= 0.437 Chirality : 0.059 0.602 2761 Planarity : 0.007 0.033 689 Dihedral : 26.643 177.424 8370 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 7.07 % Allowed : 29.29 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.77), residues: 114 helix: 0.11 (0.68), residues: 48 sheet: 0.72 (0.84), residues: 29 loop : 0.36 (1.19), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.015 0.004 TYR B 94 PHE 0.017 0.004 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.47 (13558) covalent geometry : angle 0.82366 / 0.44 (20928) hydrogen bonds : bond 0.11597 / 12.63 ( 512) hydrogen bonds : angle 2.63510 / 3.30 ( 917) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.155 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 24 average time/residue: 0.9003 time to fit residues: 22.8148 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 40.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.093251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056670 restraints weight = 38677.748| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 0.99 r_work: 0.2977 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 13558 Z= 0.452 Angle : 0.784 8.963 20928 Z= 0.419 Chirality : 0.056 0.557 2761 Planarity : 0.007 0.031 689 Dihedral : 26.601 177.039 8370 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.80), residues: 114 helix: 0.41 (0.71), residues: 48 sheet: 1.15 (0.88), residues: 29 loop : 0.35 (1.22), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.022 0.004 TYR B 94 PHE 0.016 0.004 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.45 (13558) covalent geometry : angle 0.78381 / 0.42 (20928) hydrogen bonds : bond 0.10253 / 11.37 ( 512) hydrogen bonds : angle 2.55336 / 3.23 ( 917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.105 Fit side-chains REVERT: B 12 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8716 (mt-10) outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.8280 time to fit residues: 18.3806 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 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 = 0.3991 r_free = 0.3991 target = 0.091117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053016 restraints weight = 36903.091| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.27 r_work: 0.2836 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 13558 Z= 0.556 Angle : 0.907 9.548 20928 Z= 0.470 Chirality : 0.065 0.662 2761 Planarity : 0.008 0.035 689 Dihedral : 26.602 177.937 8370 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.79), residues: 114 helix: -0.01 (0.69), residues: 48 sheet: 1.03 (0.88), residues: 29 loop : 0.29 (1.23), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.018 0.004 TYR B 94 PHE 0.015 0.005 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00869 / 0.56 (13558) covalent geometry : angle 0.90673 / 0.47 (20928) hydrogen bonds : bond 0.12745 / 13.90 ( 512) hydrogen bonds : angle 2.64702 / 3.35 ( 917) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.128 Fit side-chains REVERT: B 12 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: B 86 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8792 (mtp85) outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.7868 time to fit residues: 17.4927 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.092044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054180 restraints weight = 36911.957| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 0.83 r_work: 0.2862 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13558 Z= 0.345 Angle : 0.695 8.406 20928 Z= 0.384 Chirality : 0.050 0.511 2761 Planarity : 0.006 0.029 689 Dihedral : 26.566 176.700 8370 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.81 (0.80), residues: 114 helix: 0.84 (0.73), residues: 48 sheet: 0.37 (0.87), residues: 31 loop : 0.57 (1.26), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.017 0.003 TYR B 94 PHE 0.013 0.003 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.34 (13558) covalent geometry : angle 0.69458 / 0.38 (20928) hydrogen bonds : bond 0.09586 / 10.74 ( 512) hydrogen bonds : angle 2.48335 / 3.15 ( 917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.125 Fit side-chains REVERT: B 10 ASN cc_start: 0.9028 (t0) cc_final: 0.8727 (t0) REVERT: B 12 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8723 (mt-10) outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.7321 time to fit residues: 17.0787 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 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 = 0.3992 r_free = 0.3992 target = 0.091229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053156 restraints weight = 36828.076| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.26 r_work: 0.2831 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 13558 Z= 0.536 Angle : 0.883 9.118 20928 Z= 0.459 Chirality : 0.064 0.642 2761 Planarity : 0.007 0.032 689 Dihedral : 26.542 177.668 8370 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.06 % Allowed : 30.30 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.80), residues: 114 helix: 0.24 (0.71), residues: 48 sheet: 0.35 (0.88), residues: 31 loop : 0.50 (1.26), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.020 0.004 TYR B 94 PHE 0.014 0.004 PHE B 68 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.54 (13558) covalent geometry : angle 0.88274 / 0.46 (20928) hydrogen bonds : bond 0.12105 / 13.30 ( 512) hydrogen bonds : angle 2.62044 / 3.31 ( 917) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.154 Fit side-chains REVERT: B 10 ASN cc_start: 0.9051 (t0) cc_final: 0.8748 (t0) REVERT: B 12 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: B 86 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8779 (mtp85) outliers start: 6 outliers final: 4 residues processed: 22 average time/residue: 0.7423 time to fit residues: 17.5048 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.091359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053316 restraints weight = 36936.922| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.13 r_work: 0.2841 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 13558 Z= 0.489 Angle : 0.819 9.024 20928 Z= 0.433 Chirality : 0.060 0.588 2761 Planarity : 0.007 0.033 689 Dihedral : 26.573 177.419 8370 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: 0.43 (0.80), residues: 114 helix: 0.38 (0.71), residues: 48 sheet: 0.25 (0.87), residues: 31 loop : 0.54 (1.26), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 86 TYR 0.019 0.004 TYR B 94 PHE 0.014 0.004 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.49 (13558) covalent geometry : angle 0.81885 / 0.43 (20928) hydrogen bonds : bond 0.11123 / 12.34 ( 512) hydrogen bonds : angle 2.59900 / 3.28 ( 917) ********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.193 Fit side-chains REVERT: B 10 ASN cc_start: 0.9009 (t0) cc_final: 0.8732 (t0) REVERT: B 12 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: B 86 ARG cc_start: 0.9002 (mmm-85) cc_final: 0.8482 (mtm-85) outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.7616 time to fit residues: 17.8609 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 40.0000 chunk 1 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 overall best weight: 5.5592 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.090936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052845 restraints weight = 36792.735| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.26 r_work: 0.2823 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 13558 Z= 0.564 Angle : 0.926 9.447 20928 Z= 0.479 Chirality : 0.066 0.669 2761 Planarity : 0.008 0.035 689 Dihedral : 26.593 178.035 8370 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.05 % Allowed : 32.32 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.78), residues: 114 helix: 0.17 (0.71), residues: 48 sheet: 0.84 (0.89), residues: 29 loop : -0.08 (1.17), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.023 0.005 TYR B 94 PHE 0.015 0.005 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.56 (13558) covalent geometry : angle 0.92561 / 0.48 (20928) hydrogen bonds : bond 0.12849 / 14.09 ( 512) hydrogen bonds : angle 2.70629 / 3.42 ( 917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5068.85 seconds wall clock time: 86 minutes 43.18 seconds (5203.18 seconds total)