Starting phenix.real_space_refine on Fri Jul 3 05:08:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owx_70947/07_2026/9owx_70947_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owx_70947/07_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_70947/07_2026/9owx_70947_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owx_70947/07_2026/9owx_70947_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9owx_70947/07_2026/9owx_70947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owx_70947/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 26} Chain breaks: 26 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.91, per 1000 atoms: 0.24 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: 0.98 Conformation dependent library (CDL) restraints added in 203.0 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 44.0% alpha, 16.4% beta 183 base pairs and 313 stacking pairs defined. Time for finding SS restraints: 2.13 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: 3.05 Time building geometry restraints manager: 1.36 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 1.50e-02 4.44e+03 6.14e+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: 19234 3.01 - 6.02: 1518 6.02 - 9.03: 165 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 1.50e+00 4.44e-01 1.01e+02 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=" O3' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " ideal model delta sigma weight residual 109.50 118.79 -9.29 1.50e+00 4.44e-01 3.84e+01 angle pdb=" O3' C C -5 " pdb=" P C C -4 " pdb=" O5' C C -4 " ideal model delta sigma weight residual 104.00 94.76 9.24 1.50e+00 4.44e-01 3.79e+01 angle pdb=" C4' C A 182 " pdb=" C3' C A 182 " pdb=" C2' C A 182 " ideal model delta sigma weight residual 102.60 96.69 5.91 1.00e+00 1.00e+00 3.49e+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: 1948 0.125 - 0.249: 441 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 3.250 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: 4.550 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: 0.040 Set scattering table: 0.040 Process input model: 14.130 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- 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= 0.700 Angle : 1.641 15.045 20928 Z= 0.974 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 0.00982 / 0.70 (13558) covalent geometry : angle 1.64123 / 0.97 (20928) hydrogen bonds : bond 0.20255 / 18.16 ( 512) hydrogen bonds : angle 8.89478 / 10.81 ( 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 : 0.170 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: 0.8171 time to fit residues: 29.5962 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 : 0.168 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.093584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055555 restraints weight = 36617.351| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.58 r_work: 0.2907 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 13558 Z= 0.463 Angle : 0.745 7.598 20928 Z= 0.448 Chirality : 0.056 0.455 2761 Planarity : 0.007 0.031 689 Dihedral : 27.178 177.648 8378 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 13.13 % Allowed : 16.16 % 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: 1.16 (0.80), residues: 114 helix: 1.07 (0.73), residues: 48 sheet: 0.98 (0.90), residues: 30 loop : 0.40 (1.20), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.009 0.003 TYR B 94 PHE 0.016 0.004 PHE B 68 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.46 (13558) covalent geometry : angle 0.74538 / 0.45 (20928) hydrogen bonds : bond 0.11501 / 11.36 ( 512) hydrogen bonds : angle 2.75881 / 3.29 ( 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.171 Fit side-chains REVERT: B 12 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8737 (mt-10) outliers start: 13 outliers final: 7 residues processed: 29 average time/residue: 0.9333 time to fit residues: 28.6655 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.092042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053864 restraints weight = 36801.104| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.58 r_work: 0.2859 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 13558 Z= 0.567 Angle : 0.769 11.276 20928 Z= 0.458 Chirality : 0.057 0.490 2761 Planarity : 0.007 0.039 689 Dihedral : 26.919 176.736 8374 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: 0.40 (0.83), residues: 114 helix: -0.08 (0.70), residues: 47 sheet: 0.43 (0.81), residues: 29 loop : 0.99 (1.36), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 86 TYR 0.012 0.004 TYR B 31 PHE 0.018 0.005 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00920 / 0.57 (13558) covalent geometry : angle 0.76861 / 0.46 (20928) hydrogen bonds : bond 0.13229 / 12.94 ( 512) hydrogen bonds : angle 2.87454 / 3.30 ( 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.225 Fit side-chains REVERT: B 38 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8180 (tt0) outliers start: 12 outliers final: 7 residues processed: 26 average time/residue: 0.9131 time to fit residues: 25.2741 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.092721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054821 restraints weight = 36625.847| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.28 r_work: 0.2887 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13558 Z= 0.393 Angle : 0.611 9.280 20928 Z= 0.379 Chirality : 0.047 0.392 2761 Planarity : 0.006 0.031 689 Dihedral : 26.828 175.571 8374 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 11.11 % Allowed : 22.22 % 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: 0.80 (0.80), residues: 114 helix: 0.86 (0.73), residues: 48 sheet: 0.48 (0.79), residues: 29 loop : 0.40 (1.28), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.015 0.003 TYR B 94 PHE 0.011 0.003 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.39 (13558) covalent geometry : angle 0.61103 / 0.38 (20928) hydrogen bonds : bond 0.09264 / 9.30 ( 512) hydrogen bonds : angle 2.55169 / 2.94 ( 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.122 Fit side-chains REVERT: B 12 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: B 38 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: B 112 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7989 (mptp) outliers start: 11 outliers final: 5 residues processed: 25 average time/residue: 0.8688 time to fit residues: 22.9441 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 38 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 ARG Chi-restraints excluded: chain B residue 112 LYS 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: 30.0000 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 44 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 4.0386 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.093346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056026 restraints weight = 36763.842| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.42 r_work: 0.2996 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 13558 Z= 0.478 Angle : 0.676 12.349 20928 Z= 0.408 Chirality : 0.052 0.443 2761 Planarity : 0.007 0.037 689 Dihedral : 26.722 176.423 8370 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 10.10 % Allowed : 25.25 % 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: 0.88 (0.80), residues: 114 helix: 0.80 (0.71), residues: 48 sheet: 0.85 (0.80), residues: 29 loop : 0.32 (1.27), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.015 0.003 TYR B 94 PHE 0.014 0.004 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.48 (13558) covalent geometry : angle 0.67641 / 0.41 (20928) hydrogen bonds : bond 0.11091 / 10.94 ( 512) hydrogen bonds : angle 2.56833 / 2.91 ( 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.162 Fit side-chains REVERT: B 12 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8637 (mt-10) REVERT: B 112 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7980 (mptp) outliers start: 10 outliers final: 5 residues processed: 25 average time/residue: 0.9219 time to fit residues: 24.3100 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 106 ARG Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.094217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.057919 restraints weight = 38747.993| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.29 r_work: 0.2999 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13558 Z= 0.376 Angle : 0.591 10.186 20928 Z= 0.362 Chirality : 0.046 0.387 2761 Planarity : 0.006 0.027 689 Dihedral : 26.670 176.658 8370 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 7.07 % Allowed : 27.27 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.81), residues: 114 helix: 1.06 (0.74), residues: 47 sheet: 0.66 (0.78), residues: 29 loop : 0.81 (1.28), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 86 TYR 0.023 0.004 TYR B 94 PHE 0.015 0.003 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.38 (13558) covalent geometry : angle 0.59080 / 0.36 (20928) hydrogen bonds : bond 0.08623 / 8.80 ( 512) hydrogen bonds : angle 2.42063 / 2.74 ( 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.170 Fit side-chains REVERT: B 38 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8194 (tt0) outliers start: 7 outliers final: 4 residues processed: 23 average time/residue: 0.8733 time to fit residues: 21.3549 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 106 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.093261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.056658 restraints weight = 38579.420| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.64 r_work: 0.2970 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 13558 Z= 0.500 Angle : 0.666 10.035 20928 Z= 0.403 Chirality : 0.052 0.449 2761 Planarity : 0.007 0.034 689 Dihedral : 26.622 176.882 8368 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.07 % Allowed : 27.27 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.80), residues: 114 helix: 0.66 (0.72), residues: 47 sheet: 0.86 (0.81), residues: 29 loop : 0.59 (1.27), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.017 0.004 TYR B 40 PHE 0.014 0.004 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00820 / 0.50 (13558) covalent geometry : angle 0.66612 / 0.40 (20928) hydrogen bonds : bond 0.10742 / 10.72 ( 512) hydrogen bonds : angle 2.50956 / 2.84 ( 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: 7 poor density : 15 time to evaluate : 0.109 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 21 average time/residue: 0.8710 time to fit residues: 19.3869 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 106 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.092733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054859 restraints weight = 36948.974| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.07 r_work: 0.2882 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13558 Z= 0.315 Angle : 0.551 9.821 20928 Z= 0.344 Chirality : 0.042 0.369 2761 Planarity : 0.005 0.028 689 Dihedral : 26.630 176.810 8368 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.05 % Allowed : 29.29 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.81), residues: 114 helix: 1.27 (0.76), residues: 47 sheet: 0.81 (0.79), residues: 29 loop : 0.56 (1.24), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.015 0.002 TYR B 94 PHE 0.011 0.003 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.32 (13558) covalent geometry : angle 0.55062 / 0.34 (20928) hydrogen bonds : bond 0.08561 / 8.81 ( 512) hydrogen bonds : angle 2.38002 / 2.71 ( 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.168 Fit side-chains REVERT: B 10 ASN cc_start: 0.9037 (t0) cc_final: 0.8685 (t0) outliers start: 5 outliers final: 4 residues processed: 20 average time/residue: 0.8819 time to fit residues: 18.8168 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 : 0.163 ------------------------------------------------------------------------------- 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 106 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.091916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054109 restraints weight = 36872.367| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.41 r_work: 0.2864 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13558 Z= 0.431 Angle : 0.618 8.912 20928 Z= 0.379 Chirality : 0.049 0.429 2761 Planarity : 0.006 0.031 689 Dihedral : 26.579 176.761 8368 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.04 % Allowed : 31.31 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.79), residues: 114 helix: 1.00 (0.74), residues: 47 sheet: 0.79 (0.80), residues: 29 loop : 0.44 (1.21), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.015 0.003 TYR B 94 PHE 0.011 0.003 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.43 (13558) covalent geometry : angle 0.61798 / 0.38 (20928) hydrogen bonds : bond 0.10363 / 10.48 ( 512) hydrogen bonds : angle 2.46812 / 2.79 ( 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.153 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 21 average time/residue: 0.9067 time to fit residues: 20.2920 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 106 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.091607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053622 restraints weight = 37050.225| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.46 r_work: 0.2850 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 13558 Z= 0.478 Angle : 0.659 7.206 20928 Z= 0.401 Chirality : 0.051 0.442 2761 Planarity : 0.007 0.029 689 Dihedral : 26.654 176.906 8368 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.58 (0.78), residues: 114 helix: 0.40 (0.72), residues: 47 sheet: 0.73 (0.82), residues: 29 loop : 0.36 (1.19), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 86 TYR 0.011 0.003 TYR B 94 PHE 0.015 0.004 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.48 (13558) covalent geometry : angle 0.65881 / 0.40 (20928) hydrogen bonds : bond 0.10775 / 11.00 ( 512) hydrogen bonds : angle 2.57737 / 2.87 ( 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.181 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.9206 time to fit residues: 20.5849 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 : 0.176 ------------------------------------------------------------------------------- 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 106 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 58 optimal weight: 40.0000 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.091102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053253 restraints weight = 36860.364| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.70 r_work: 0.2834 rms_B_bonded: 2.87 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: 0.8969 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 13558 Z= 0.555 Angle : 0.713 7.088 20928 Z= 0.429 Chirality : 0.056 0.483 2761 Planarity : 0.007 0.035 689 Dihedral : 26.673 177.279 8368 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.63 (0.81), residues: 114 helix: 0.56 (0.73), residues: 47 sheet: 0.70 (0.91), residues: 29 loop : 0.27 (1.20), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 86 TYR 0.019 0.004 TYR B 94 PHE 0.012 0.004 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.56 (13558) covalent geometry : angle 0.71281 / 0.43 (20928) hydrogen bonds : bond 0.12097 / 12.12 ( 512) hydrogen bonds : angle 2.56558 / 2.83 ( 917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5483.90 seconds wall clock time: 94 minutes 2.54 seconds (5642.54 seconds total)