Starting phenix.real_space_refine on Fri Jul 3 11:17:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uo5_26640/07_2026/7uo5_26640.cif" } resolution = 3.1 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= 0.013 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: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 P 372 5.49 5 S 2 5.16 5 C 4156 2.51 5 N 1688 2.21 5 O 2730 1.98 5 H 5024 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 13979 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1898 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 12074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 12074 Classifications: {'RNA': 373} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 33, 'rna2p_pyr': 32, 'rna3p_pur': 185, 'rna3p_pyr': 123} Link IDs: {'rna2p': 64, 'rna3p': 308} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 47 residue: pdb=" P C B 20 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 20 " occ=0.00 residue: pdb=" P C B 21 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 21 " occ=0.00 residue: pdb=" P G B 22 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 22 " occ=0.00 residue: pdb=" P C B 23 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 23 " occ=0.00 residue: pdb=" P U B 24 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 24 " occ=0.00 residue: pdb=" P U B 25 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 25 " occ=0.00 residue: pdb=" P C B 26 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 26 " occ=0.00 residue: pdb=" P G B 27 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 27 " occ=0.00 residue: pdb=" P U B 28 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 28 " occ=0.00 residue: pdb=" P C B 29 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 29 " occ=0.00 residue: pdb=" P G B 30 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 30 " occ=0.00 residue: pdb=" P U B 31 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 31 " occ=0.00 ... (remaining 35 not shown) Time building chain proxies: 2.21, per 1000 atoms: 0.16 Number of scatterers: 13979 At special positions: 0 Unit cell: (89.7768, 120.107, 189.259, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 2 16.00 P 372 15.00 O 2730 8.00 N 1688 7.00 C 4156 6.00 H 5024 1.00 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: 1.01 Conformation dependent library (CDL) restraints added in 187.2 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 214 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 45.5% alpha, 17.9% beta 96 base pairs and 146 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.602A pdb=" N PHE A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.934A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 93 removed outlier: 4.302A pdb=" N ALA A 93 " --> pdb=" O LYS A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.932A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.511A pdb=" N ARG A 45 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 86 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ALA A 88 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 49 " --> pdb=" O ALA A 88 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 93 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 440 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 146 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 5023 1.11 - 1.29: 488 1.29 - 1.46: 5570 1.46 - 1.64: 3868 1.64 - 1.81: 3 Bond restraints: 14952 Sorted by residual: bond pdb=" C5 C B 10 " pdb=" H5 C B 10 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CD2 PHE A 84 " pdb=" HD2 PHE A 84 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C5 C B 252 " pdb=" H5 C B 252 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C2 A B 139 " pdb=" H2 A B 139 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C6 C B 253 " pdb=" H6 C B 253 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 14947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 23959 3.22 - 6.44: 2518 6.44 - 9.66: 263 9.66 - 12.88: 23 12.88 - 16.10: 2 Bond angle restraints: 26765 Sorted by residual: angle pdb=" O3' G B 329 " pdb=" C3' G B 329 " pdb=" C2' G B 329 " ideal model delta sigma weight residual 109.50 125.60 -16.10 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O3' G B 133 " pdb=" C3' G B 133 " pdb=" C2' G B 133 " ideal model delta sigma weight residual 109.50 123.51 -14.01 1.50e+00 4.44e-01 8.73e+01 angle pdb=" O4' G B 137 " pdb=" C1' G B 137 " pdb=" C2' G B 137 " ideal model delta sigma weight residual 107.60 98.64 8.96 1.00e+00 1.00e+00 8.03e+01 angle pdb=" C4' G B 175 " pdb=" O4' G B 175 " pdb=" C1' G B 175 " ideal model delta sigma weight residual 109.90 101.17 8.73 1.00e+00 1.00e+00 7.63e+01 angle pdb=" O3' A B 173 " pdb=" C3' A B 173 " pdb=" C2' A B 173 " ideal model delta sigma weight residual 109.50 121.88 -12.38 1.50e+00 4.44e-01 6.81e+01 ... (remaining 26760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 5375 35.99 - 71.98: 474 71.98 - 107.97: 126 107.97 - 143.96: 24 143.96 - 179.95: 42 Dihedral angle restraints: 6041 sinusoidal: 5667 harmonic: 374 Sorted by residual: dihedral pdb=" C5' A B 139 " pdb=" C4' A B 139 " pdb=" C3' A B 139 " pdb=" O3' A B 139 " ideal model delta sinusoidal sigma weight residual 147.00 61.67 85.33 1 8.00e+00 1.56e-02 1.38e+02 dihedral pdb=" C5' C B 122 " pdb=" C4' C B 122 " pdb=" C3' C B 122 " pdb=" O3' C B 122 " ideal model delta sinusoidal sigma weight residual 147.00 67.95 79.05 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" C5' A B 351 " pdb=" C4' A B 351 " pdb=" C3' A B 351 " pdb=" O3' A B 351 " ideal model delta sinusoidal sigma weight residual 147.00 68.43 78.57 1 8.00e+00 1.56e-02 1.20e+02 ... (remaining 6038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 1885 0.204 - 0.408: 90 0.408 - 0.611: 23 0.611 - 0.815: 4 0.815 - 1.019: 1 Chirality restraints: 2003 Sorted by residual: chirality pdb=" P C B 145 " pdb=" OP1 C B 145 " pdb=" OP2 C B 145 " pdb=" O5' C B 145 " both_signs ideal model delta sigma weight residual True 2.41 -1.39 1.02 2.00e-01 2.50e+01 2.59e+01 chirality pdb=" C3' G B 329 " pdb=" C4' G B 329 " pdb=" O3' G B 329 " pdb=" C2' G B 329 " both_signs ideal model delta sigma weight residual False -2.74 -1.94 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C3' A B 192 " pdb=" C4' A B 192 " pdb=" O3' A B 192 " pdb=" C2' A B 192 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 2000 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 145 " 0.971 2.00e-02 2.50e+03 3.80e-01 3.97e+03 pdb=" N1 C B 145 " -0.066 2.00e-02 2.50e+03 pdb=" C2 C B 145 " -0.167 2.00e-02 2.50e+03 pdb=" O2 C B 145 " -0.557 2.00e-02 2.50e+03 pdb=" N3 C B 145 " 0.079 2.00e-02 2.50e+03 pdb=" C4 C B 145 " 0.134 2.00e-02 2.50e+03 pdb=" N4 C B 145 " 0.343 2.00e-02 2.50e+03 pdb=" C5 C B 145 " -0.106 2.00e-02 2.50e+03 pdb=" C6 C B 145 " -0.216 2.00e-02 2.50e+03 pdb=" H5 C B 145 " -0.120 2.00e-02 2.50e+03 pdb=" H6 C B 145 " -0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 336 " 0.672 2.00e-02 2.50e+03 2.38e-01 1.98e+03 pdb=" N9 G B 336 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G B 336 " -0.141 2.00e-02 2.50e+03 pdb=" N7 G B 336 " -0.172 2.00e-02 2.50e+03 pdb=" C5 G B 336 " -0.097 2.00e-02 2.50e+03 pdb=" C6 G B 336 " 0.076 2.00e-02 2.50e+03 pdb=" O6 G B 336 " 0.282 2.00e-02 2.50e+03 pdb=" N1 G B 336 " 0.044 2.00e-02 2.50e+03 pdb=" C2 G B 336 " -0.167 2.00e-02 2.50e+03 pdb=" N2 G B 336 " -0.129 2.00e-02 2.50e+03 pdb=" N3 G B 336 " -0.246 2.00e-02 2.50e+03 pdb=" C4 G B 336 " -0.187 2.00e-02 2.50e+03 pdb=" H8 G B 336 " -0.121 2.00e-02 2.50e+03 pdb=" H1 G B 336 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 144 " 0.603 2.00e-02 2.50e+03 2.26e-01 1.78e+03 pdb=" N9 G B 144 " 0.017 2.00e-02 2.50e+03 pdb=" C8 G B 144 " -0.192 2.00e-02 2.50e+03 pdb=" N7 G B 144 " -0.149 2.00e-02 2.50e+03 pdb=" C5 G B 144 " -0.042 2.00e-02 2.50e+03 pdb=" C6 G B 144 " 0.119 2.00e-02 2.50e+03 pdb=" O6 G B 144 " 0.350 2.00e-02 2.50e+03 pdb=" N1 G B 144 " 0.061 2.00e-02 2.50e+03 pdb=" C2 G B 144 " -0.084 2.00e-02 2.50e+03 pdb=" N2 G B 144 " -0.250 2.00e-02 2.50e+03 pdb=" N3 G B 144 " -0.082 2.00e-02 2.50e+03 pdb=" C4 G B 144 " -0.078 2.00e-02 2.50e+03 pdb=" H8 G B 144 " -0.258 2.00e-02 2.50e+03 pdb=" H1 G B 144 " -0.013 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 790 2.08 - 2.71: 14734 2.71 - 3.34: 35932 3.34 - 3.97: 54135 3.97 - 4.60: 74342 Nonbonded interactions: 179933 Sorted by model distance: nonbonded pdb="HO2' C B 343 " pdb=" H3' A B 344 " model vdw 1.453 2.270 nonbonded pdb="HO2' A B 181 " pdb=" OP2 A B 182 " model vdw 1.497 2.450 nonbonded pdb=" OP1 C B 145 " pdb="HO2' G B 147 " model vdw 1.562 2.450 nonbonded pdb="HO2' A B 193 " pdb=" OP1 G B 194 " model vdw 1.565 2.450 nonbonded pdb="HO2' G B 165 " pdb=" OP1 A B 166 " model vdw 1.566 2.450 ... (remaining 179928 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=0.00 max=1.00 mean=0.89 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: 4.130 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: 0.040 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 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 : 0.015 0.063 9928 Z= 0.869 Angle : 2.219 16.101 15291 Z= 1.426 Chirality : 0.120 1.019 2003 Planarity : 0.058 0.386 538 Dihedral : 27.597 179.953 4846 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.36 % Favored : 92.73 % Rotamer: Outliers : 1.02 % Allowed : 10.20 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.76), residues: 110 helix: -3.09 (0.62), residues: 37 sheet: 1.09 (1.36), residues: 12 loop : -1.55 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 75 PHE 0.043 0.012 PHE A 84 TRP 0.039 0.021 TRP A 108 HIS 0.007 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.01482 / 0.87 ( 9928) covalent geometry : angle 2.21925 / 1.43 (15291) hydrogen bonds : bond 0.12440 / 8.37 ( 287) hydrogen bonds : angle 8.43930 / 6.04 ( 533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.3649 time to fit residues: 10.4167 Evaluate side-chains 17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.123143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.108020 restraints weight = 122423.854| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.02 r_work: 0.3989 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9928 Z= 0.220 Angle : 1.011 9.896 15291 Z= 0.538 Chirality : 0.051 0.318 2003 Planarity : 0.007 0.036 538 Dihedral : 26.044 179.736 4601 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.91 % Allowed : 3.64 % Favored : 95.45 % Rotamer: Outliers : 1.02 % Allowed : 10.20 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.76), residues: 110 helix: -2.77 (0.53), residues: 54 sheet: 0.19 (1.07), residues: 19 loop : -1.19 (1.20), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 PHE 0.014 0.002 PHE A 84 TRP 0.002 0.001 TRP A 108 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.22 ( 9928) covalent geometry : angle 1.01134 / 0.54 (15291) hydrogen bonds : bond 0.08421 / 5.18 ( 287) hydrogen bonds : angle 3.12053 / 2.15 ( 533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.175 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.3404 time to fit residues: 7.3353 Evaluate side-chains 13 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.119966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.104960 restraints weight = 114889.485| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.60 r_work: 0.3905 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9928 Z= 0.249 Angle : 0.890 9.762 15291 Z= 0.465 Chirality : 0.046 0.311 2003 Planarity : 0.006 0.050 538 Dihedral : 25.967 179.268 4601 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.02 % Allowed : 17.35 % Favored : 81.63 % 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: -2.87 (0.74), residues: 110 helix: -2.41 (0.59), residues: 54 sheet: -0.58 (1.01), residues: 19 loop : -1.43 (1.10), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 37 PHE 0.011 0.002 PHE A 84 TRP 0.003 0.001 TRP A 108 HIS 0.008 0.003 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.25 ( 9928) covalent geometry : angle 0.88995 / 0.47 (15291) hydrogen bonds : bond 0.08990 / 5.44 ( 287) hydrogen bonds : angle 3.06991 / 2.13 ( 533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.3177 time to fit residues: 5.8992 Evaluate side-chains 15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.118445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.104065 restraints weight = 116704.989| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.68 r_work: 0.3865 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9928 Z= 0.345 Angle : 0.962 10.441 15291 Z= 0.493 Chirality : 0.050 0.348 2003 Planarity : 0.007 0.039 538 Dihedral : 26.468 178.337 4601 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 4.08 % Allowed : 17.35 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.68), residues: 110 helix: -3.14 (0.47), residues: 54 sheet: -0.93 (1.05), residues: 19 loop : -1.81 (1.06), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 37 PHE 0.010 0.002 PHE A 84 TRP 0.004 0.002 TRP A 108 HIS 0.008 0.003 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.34 ( 9928) covalent geometry : angle 0.96227 / 0.49 (15291) hydrogen bonds : bond 0.10768 / 6.67 ( 287) hydrogen bonds : angle 3.40081 / 2.48 ( 533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8343 (mtp) cc_final: 0.7917 (mtp) outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.2726 time to fit residues: 6.4418 Evaluate side-chains 16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.119375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.103242 restraints weight = 116452.840| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.09 r_work: 0.3915 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9928 Z= 0.249 Angle : 0.834 9.392 15291 Z= 0.431 Chirality : 0.044 0.305 2003 Planarity : 0.006 0.037 538 Dihedral : 26.060 179.067 4601 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 3.06 % Allowed : 18.37 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.71), residues: 110 helix: -2.93 (0.52), residues: 54 sheet: -0.48 (1.13), residues: 19 loop : -1.81 (1.04), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 37 PHE 0.010 0.002 PHE A 84 TRP 0.003 0.001 TRP A 108 HIS 0.004 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.25 ( 9928) covalent geometry : angle 0.83402 / 0.43 (15291) hydrogen bonds : bond 0.08397 / 5.23 ( 287) hydrogen bonds : angle 3.05917 / 2.18 ( 533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7933 (tp30) cc_final: 0.7195 (mm-30) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.3047 time to fit residues: 6.4151 Evaluate side-chains 16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.117688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.103655 restraints weight = 117335.484| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.73 r_work: 0.3861 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9928 Z= 0.347 Angle : 0.945 10.013 15291 Z= 0.481 Chirality : 0.049 0.347 2003 Planarity : 0.007 0.040 538 Dihedral : 26.429 179.211 4601 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.91 % Allowed : 12.73 % Favored : 86.36 % Rotamer: Outliers : 3.06 % Allowed : 19.39 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.68), residues: 110 helix: -3.43 (0.45), residues: 54 sheet: -0.45 (1.11), residues: 19 loop : -2.29 (1.02), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 37 PHE 0.010 0.002 PHE A 84 TRP 0.004 0.002 TRP A 108 HIS 0.005 0.002 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.35 ( 9928) covalent geometry : angle 0.94477 / 0.48 (15291) hydrogen bonds : bond 0.10662 / 6.60 ( 287) hydrogen bonds : angle 3.36612 / 2.48 ( 533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8181 (mtp) cc_final: 0.7783 (mtp) REVERT: A 105 GLU cc_start: 0.8044 (tp30) cc_final: 0.7280 (mm-30) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.3253 time to fit residues: 8.3772 Evaluate side-chains 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.104422 restraints weight = 115581.988| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.59 r_work: 0.3901 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9928 Z= 0.207 Angle : 0.793 9.308 15291 Z= 0.412 Chirality : 0.042 0.294 2003 Planarity : 0.005 0.037 538 Dihedral : 25.973 178.138 4601 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.18 % Favored : 90.91 % Rotamer: Outliers : 3.06 % Allowed : 19.39 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.70), residues: 110 helix: -3.12 (0.50), residues: 52 sheet: -0.71 (1.09), residues: 19 loop : -2.09 (1.02), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 37 PHE 0.007 0.001 PHE A 84 TRP 0.003 0.001 TRP A 108 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.21 ( 9928) covalent geometry : angle 0.79302 / 0.41 (15291) hydrogen bonds : bond 0.07824 / 4.84 ( 287) hydrogen bonds : angle 3.00656 / 2.15 ( 533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8052 (mtp) cc_final: 0.7678 (mtp) REVERT: A 105 GLU cc_start: 0.7955 (tp30) cc_final: 0.7207 (mm-30) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.3234 time to fit residues: 8.2735 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.118037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.103968 restraints weight = 115452.559| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.65 r_work: 0.3877 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9928 Z= 0.284 Angle : 0.855 8.883 15291 Z= 0.439 Chirality : 0.046 0.318 2003 Planarity : 0.006 0.039 538 Dihedral : 26.120 179.898 4601 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.91 % Favored : 88.18 % Rotamer: Outliers : 3.06 % Allowed : 19.39 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.69), residues: 110 helix: -3.03 (0.52), residues: 48 sheet: -1.24 (1.08), residues: 21 loop : -2.67 (0.94), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 37 PHE 0.009 0.002 PHE A 5 TRP 0.003 0.001 TRP A 108 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.28 ( 9928) covalent geometry : angle 0.85542 / 0.44 (15291) hydrogen bonds : bond 0.09230 / 5.63 ( 287) hydrogen bonds : angle 3.15038 / 2.31 ( 533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8154 (mtp) cc_final: 0.7747 (mtp) REVERT: A 105 GLU cc_start: 0.8032 (tp30) cc_final: 0.7243 (mm-30) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.2976 time to fit residues: 6.6799 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.119908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.105453 restraints weight = 117285.588| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.61 r_work: 0.3923 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9928 Z= 0.155 Angle : 0.734 8.751 15291 Z= 0.383 Chirality : 0.039 0.297 2003 Planarity : 0.005 0.040 538 Dihedral : 25.646 177.560 4601 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.91 % Allowed : 4.55 % Favored : 94.55 % Rotamer: Outliers : 2.04 % Allowed : 20.41 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.74), residues: 110 helix: -2.24 (0.63), residues: 44 sheet: -1.09 (1.11), residues: 21 loop : -1.87 (0.95), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 PHE 0.007 0.001 PHE A 19 TRP 0.001 0.001 TRP A 108 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 9928) covalent geometry : angle 0.73408 / 0.38 (15291) hydrogen bonds : bond 0.07085 / 4.27 ( 287) hydrogen bonds : angle 2.78120 / 1.97 ( 533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8082 (mtp) cc_final: 0.7677 (mtp) REVERT: A 105 GLU cc_start: 0.7983 (tp30) cc_final: 0.7164 (mm-30) outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.2394 time to fit residues: 5.6166 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.117710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.103541 restraints weight = 116829.400| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.80 r_work: 0.3867 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9928 Z= 0.339 Angle : 0.893 8.813 15291 Z= 0.453 Chirality : 0.048 0.339 2003 Planarity : 0.006 0.040 538 Dihedral : 26.029 179.648 4601 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 25.77 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.82 % Favored : 87.27 % Rotamer: Outliers : 2.04 % Allowed : 19.39 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.71), residues: 110 helix: -2.83 (0.55), residues: 46 sheet: -0.89 (1.17), residues: 21 loop : -2.57 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 37 PHE 0.011 0.002 PHE A 84 TRP 0.003 0.002 TRP A 108 HIS 0.005 0.002 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.34 ( 9928) covalent geometry : angle 0.89284 / 0.45 (15291) hydrogen bonds : bond 0.09873 / 6.04 ( 287) hydrogen bonds : angle 3.19208 / 2.37 ( 533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7720 (tp30) cc_final: 0.7463 (tp30) REVERT: A 82 MET cc_start: 0.8197 (mtp) cc_final: 0.7789 (mtp) REVERT: A 105 GLU cc_start: 0.8064 (tp30) cc_final: 0.7292 (mm-30) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.3094 time to fit residues: 6.7160 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.118127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.103883 restraints weight = 116752.910| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.65 r_work: 0.3885 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9928 Z= 0.272 Angle : 0.829 8.933 15291 Z= 0.425 Chirality : 0.044 0.314 2003 Planarity : 0.006 0.041 538 Dihedral : 25.932 179.741 4601 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.00 % Favored : 89.09 % Rotamer: Outliers : 2.04 % Allowed : 20.41 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.72), residues: 110 helix: -2.84 (0.55), residues: 46 sheet: -0.73 (1.21), residues: 21 loop : -2.55 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 37 PHE 0.008 0.002 PHE A 84 TRP 0.003 0.001 TRP A 108 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.27 ( 9928) covalent geometry : angle 0.82890 / 0.42 (15291) hydrogen bonds : bond 0.08594 / 5.27 ( 287) hydrogen bonds : angle 3.06029 / 2.26 ( 533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4910.83 seconds wall clock time: 83 minutes 57.08 seconds (5037.08 seconds total)