Starting phenix.real_space_refine on Tue Aug 4 11:43:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9peh_71562/08_2026/9peh_71562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9peh_71562/08_2026/9peh_71562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9peh_71562/08_2026/9peh_71562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9peh_71562/08_2026/9peh_71562.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9peh_71562/08_2026/9peh_71562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9peh_71562/08_2026/9peh_71562.map" } resolution = 3.7 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= 0.001 sd= 0.019 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: 3 Type Number sf(0) Gaussians C 912 2.51 5 N 176 2.21 5 O 176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1264 Number of models: 1 Model: "" Number of chains: 32 Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.21, per 1000 atoms: 0.17 Number of scatterers: 1264 At special positions: 0 Unit cell: (77.19, 79.68, 53.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 176 8.00 N 176 7.00 C 912 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 18.8 milliseconds 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 224 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.423A pdb=" N GLU J 4 " --> pdb=" O PHE B 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 3 through 5 removed outlier: 6.123A pdb=" N GLU K 4 " --> pdb=" O PHE C 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 3 through 5 removed outlier: 6.346A pdb=" N GLU L 4 " --> pdb=" O PHE D 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 2 through 6 Processing sheet with id=AA5, first strand: chain 'O' and resid 2 through 6 Processing sheet with id=AA6, first strand: chain 'Q' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'S' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'U' and resid 2 through 6 removed outlier: 3.588A pdb=" N LYS V 2 " --> pdb=" O LYS U 6 " (cutoff:3.500A) 27 hydrogen bonds defined for protein. 54 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.08 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 162 1.26 - 1.33: 88 1.33 - 1.40: 410 1.40 - 1.48: 156 1.48 - 1.55: 480 Bond restraints: 1296 Sorted by residual: bond pdb=" C PHE C 7 " pdb=" N GLY C 8 " ideal model delta sigma weight residual 1.329 1.431 -0.102 1.40e-02 5.10e+03 5.27e+01 bond pdb=" C PHE O 7 " pdb=" N GLY O 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" C PHE P 7 " pdb=" N GLY P 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" C PHE N 7 " pdb=" N GLY N 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.23e+01 bond pdb=" C PHE Q 7 " pdb=" N GLY Q 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.21e+01 ... (remaining 1291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.29: 1639 9.29 - 18.58: 13 18.58 - 27.88: 6 27.88 - 37.17: 5 37.17 - 46.46: 1 Bond angle restraints: 1664 Sorted by residual: angle pdb=" C PHE O 7 " pdb=" N GLY O 8 " pdb=" CA GLY O 8 " ideal model delta sigma weight residual 121.70 168.16 -46.46 1.80e+00 3.09e-01 6.66e+02 angle pdb=" O PHE J 7 " pdb=" C PHE J 7 " pdb=" N GLY J 8 " ideal model delta sigma weight residual 122.59 91.02 31.57 1.33e+00 5.65e-01 5.63e+02 angle pdb=" C PHE T 7 " pdb=" N GLY T 8 " pdb=" CA GLY T 8 " ideal model delta sigma weight residual 121.70 89.94 31.76 1.80e+00 3.09e-01 3.11e+02 angle pdb=" C PHE M 7 " pdb=" N GLY M 8 " pdb=" CA GLY M 8 " ideal model delta sigma weight residual 121.70 152.33 -30.63 1.80e+00 3.09e-01 2.90e+02 angle pdb=" C PHE N 7 " pdb=" N GLY N 8 " pdb=" CA GLY N 8 " ideal model delta sigma weight residual 121.70 93.39 28.31 1.80e+00 3.09e-01 2.47e+02 ... (remaining 1659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 625 36.00 - 72.00: 31 72.00 - 108.00: 0 108.00 - 143.99: 0 143.99 - 179.99: 16 Dihedral angle restraints: 672 sinusoidal: 336 harmonic: 336 Sorted by residual: dihedral pdb=" CH3 ACE O 0 " pdb=" C ACE O 0 " pdb=" N PHE O 1 " pdb=" CA PHE O 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE J 0 " pdb=" C ACE J 0 " pdb=" N PHE J 1 " pdb=" CA PHE J 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.03 -179.97 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N PHE B 1 " pdb=" CA PHE B 1 " ideal model delta sinusoidal sigma weight residual 180.00 0.09 179.91 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 669 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.029: 69 0.029 - 0.057: 34 0.057 - 0.084: 7 0.084 - 0.111: 1 0.111 - 0.139: 1 Chirality restraints: 112 Sorted by residual: chirality pdb=" CA PHE V 7 " pdb=" N PHE V 7 " pdb=" C PHE V 7 " pdb=" CB PHE V 7 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA LYS S 6 " pdb=" N LYS S 6 " pdb=" C LYS S 6 " pdb=" CB LYS S 6 " both_signs ideal model delta sigma weight residual False 2.51 2.60 -0.08 2.00e-01 2.50e+01 1.80e-01 chirality pdb=" CA PHE S 3 " pdb=" N PHE S 3 " pdb=" C PHE S 3 " pdb=" CB PHE S 3 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.65e-01 ... (remaining 109 not shown) Planarity restraints: 208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J 7 " 0.108 2.00e-02 2.50e+03 1.70e-01 2.90e+02 pdb=" C PHE J 7 " -0.295 2.00e-02 2.50e+03 pdb=" O PHE J 7 " 0.099 2.00e-02 2.50e+03 pdb=" N GLY J 8 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 7 " -0.067 2.00e-02 2.50e+03 1.28e-01 1.63e+02 pdb=" C PHE B 7 " 0.221 2.00e-02 2.50e+03 pdb=" O PHE B 7 " -0.088 2.00e-02 2.50e+03 pdb=" N GLY B 8 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 7 " 0.072 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C PHE C 7 " -0.212 2.00e-02 2.50e+03 pdb=" O PHE C 7 " 0.074 2.00e-02 2.50e+03 pdb=" N GLY C 8 " 0.065 2.00e-02 2.50e+03 ... (remaining 205 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 525 2.89 - 3.39: 843 3.39 - 3.89: 1670 3.89 - 4.40: 1755 4.40 - 4.90: 3128 Nonbonded interactions: 7921 Sorted by model distance: nonbonded pdb=" O LYS U 6 " pdb=" N GLY U 8 " model vdw 2.386 3.120 nonbonded pdb=" O PHE T 7 " pdb=" CA GLY T 8 " model vdw 2.449 2.752 nonbonded pdb=" O PHE N 7 " pdb=" CA GLY N 8 " model vdw 2.464 2.752 nonbonded pdb=" O PHE P 7 " pdb=" CA GLY P 8 " model vdw 2.468 2.752 nonbonded pdb=" O LYS V 6 " pdb=" N GLY V 8 " model vdw 2.471 3.120 ... (remaining 7916 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 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 : 0.020 0.135 1312 Z= 1.120 Angle : 3.225 46.462 1664 Z= 1.803 Chirality : 0.036 0.139 112 Planarity : 0.021 0.170 208 Dihedral : 38.082 179.992 448 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 2.08 % Allowed : 13.54 % Favored : 84.38 % Rotamer: Outliers : 4.46 % Allowed : 16.96 % 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: -4.57 (0.58), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.44), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE V 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01963 / 1.10 ( 1296) covalent geometry : angle 3.22486 / 1.80 ( 1664) hydrogen bonds : bond 0.23724 / 12.50 ( 27) hydrogen bonds : angle 21.03101 / 12.85 ( 54) Misc. bond : bond 0.02104 / 1.04 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.028 Fit side-chains REVERT: L 2 LYS cc_start: 0.8578 (tttm) cc_final: 0.8203 (mmmt) REVERT: M 1 PHE cc_start: 0.7455 (m-80) cc_final: 0.4783 (p90) outliers start: 5 outliers final: 0 residues processed: 32 average time/residue: 0.0571 time to fit residues: 1.9745 Evaluate side-chains 20 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.090305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082075 restraints weight = 4720.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083381 restraints weight = 2838.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084271 restraints weight = 1930.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084984 restraints weight = 1424.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085493 restraints weight = 1111.819| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.9871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.085 0.463 1312 Z= 3.572 Angle : 4.122 25.733 1664 Z= 2.099 Chirality : 0.248 0.958 112 Planarity : 0.022 0.062 208 Dihedral : 14.825 51.331 144 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 117.02 Ramachandran Plot: Outliers : 5.21 % Allowed : 45.83 % Favored : 48.96 % Rotamer: Outliers : 29.46 % Allowed : 25.89 % Favored : 44.64 % Cbeta Deviations : 6.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % 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: -9.11 (0.42), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.32), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.018 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08559 / 3.59 ( 1296) covalent geometry : angle 4.12202 / 2.10 ( 1664) hydrogen bonds : bond 0.34769 / 20.42 ( 27) hydrogen bonds : angle 19.77943 / 12.51 ( 54) Misc. bond : bond 0.00480 / 0.25 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 20 time to evaluate : 0.034 Fit side-chains REVERT: J 2 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8392 (tppt) REVERT: J 6 LYS cc_start: 0.9116 (tttm) cc_final: 0.8575 (tppt) REVERT: B 6 LYS cc_start: 0.5190 (pttm) cc_final: 0.3648 (pttm) REVERT: K 2 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8126 (tppt) REVERT: K 4 GLU cc_start: 0.7789 (tt0) cc_final: 0.7521 (tm-30) REVERT: K 6 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.4759 (mmtt) REVERT: C 2 LYS cc_start: 0.8920 (tttm) cc_final: 0.8467 (ttpt) REVERT: L 2 LYS cc_start: 0.9019 (tttm) cc_final: 0.8286 (mmmt) REVERT: L 3 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: L 6 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8879 (mmmt) REVERT: D 3 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: D 6 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8629 (pttm) REVERT: M 1 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: O 3 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9090 (m-80) REVERT: P 1 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: Q 3 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8799 (m-10) REVERT: R 1 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8930 (m-80) REVERT: S 7 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7846 (t80) outliers start: 33 outliers final: 12 residues processed: 47 average time/residue: 0.0583 time to fit residues: 2.9654 Evaluate side-chains 44 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 20 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 3 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.090570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082022 restraints weight = 4401.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083269 restraints weight = 2686.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084190 restraints weight = 1857.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084837 restraints weight = 1379.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085219 restraints weight = 1092.055| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 1.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.474 1312 Z= 3.537 Angle : 4.018 21.701 1664 Z= 2.089 Chirality : 0.233 0.947 112 Planarity : 0.020 0.062 208 Dihedral : 15.433 52.255 144 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 114.47 Ramachandran Plot: Outliers : 2.08 % Allowed : 62.50 % Favored : 35.42 % Rotamer: Outliers : 41.96 % Allowed : 23.21 % Favored : 34.82 % Cbeta Deviations : 5.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.25 % 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: -9.76 (0.33), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.44 (0.25), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08499 / 3.56 ( 1296) covalent geometry : angle 4.01849 / 2.09 ( 1664) hydrogen bonds : bond 0.38345 / 22.95 ( 27) hydrogen bonds : angle 19.34525 / 12.22 ( 54) Misc. bond : bond 0.00518 / 0.26 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 15 time to evaluate : 0.062 Fit side-chains REVERT: J 1 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8050 (t80) REVERT: J 2 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8352 (tppt) REVERT: J 6 LYS cc_start: 0.9113 (tttm) cc_final: 0.8599 (tppt) REVERT: B 6 LYS cc_start: 0.4755 (OUTLIER) cc_final: 0.3241 (pttm) REVERT: K 2 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8194 (tppt) REVERT: K 4 GLU cc_start: 0.8002 (tt0) cc_final: 0.7595 (tm-30) REVERT: K 6 LYS cc_start: 0.4844 (OUTLIER) cc_final: 0.2865 (mmtm) REVERT: C 2 LYS cc_start: 0.8898 (tttm) cc_final: 0.8554 (ttpt) REVERT: C 6 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8410 (pttp) REVERT: L 2 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8361 (mmmt) REVERT: L 3 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: L 6 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8887 (mmmt) REVERT: D 3 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: D 4 GLU cc_start: 0.5360 (OUTLIER) cc_final: 0.5045 (pm20) REVERT: D 6 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8649 (pttm) REVERT: M 1 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: O 1 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: O 3 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.9032 (m-80) REVERT: O 7 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: P 6 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7971 (mtpp) REVERT: P 7 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7822 (t80) REVERT: Q 3 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8858 (m-10) REVERT: Q 5 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8844 (m-10) REVERT: Q 6 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8242 (mtmt) REVERT: S 7 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7689 (t80) REVERT: V 7 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6283 (m-80) outliers start: 47 outliers final: 18 residues processed: 57 average time/residue: 0.0960 time to fit residues: 5.8611 Evaluate side-chains 54 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 15 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 7 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 3 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.089410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.080504 restraints weight = 4611.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081715 restraints weight = 2925.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082612 restraints weight = 2082.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083171 restraints weight = 1589.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083633 restraints weight = 1289.416| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 1.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.504 1312 Z= 3.520 Angle : 3.934 21.423 1664 Z= 2.048 Chirality : 0.231 0.970 112 Planarity : 0.020 0.062 208 Dihedral : 15.957 52.730 144 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 118.15 Ramachandran Plot: Outliers : 2.08 % Allowed : 64.58 % Favored : 33.33 % Rotamer: Outliers : 45.54 % Allowed : 23.21 % Favored : 31.25 % Cbeta Deviations : 6.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.14 % 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: -9.95 (0.27), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.58 (0.21), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08452 / 3.54 ( 1296) covalent geometry : angle 3.93424 / 2.05 ( 1664) hydrogen bonds : bond 0.39431 / 23.48 ( 27) hydrogen bonds : angle 19.10546 / 12.04 ( 54) Misc. bond : bond 0.00457 / 0.25 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 15 time to evaluate : 0.058 Fit side-chains REVERT: J 1 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8027 (t80) REVERT: J 2 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8385 (tppt) REVERT: J 6 LYS cc_start: 0.9126 (tttm) cc_final: 0.8610 (tppt) REVERT: K 2 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8211 (tppt) REVERT: K 4 GLU cc_start: 0.8063 (tt0) cc_final: 0.7587 (tm-30) REVERT: K 6 LYS cc_start: 0.4870 (OUTLIER) cc_final: 0.2806 (mmtm) REVERT: C 2 LYS cc_start: 0.8919 (tttm) cc_final: 0.8604 (ttmt) REVERT: C 6 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8376 (pttp) REVERT: L 2 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8255 (mmmt) REVERT: L 3 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: L 6 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8898 (mmmt) REVERT: D 3 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: D 4 GLU cc_start: 0.5337 (OUTLIER) cc_final: 0.5121 (pm20) REVERT: D 6 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8576 (pttm) REVERT: M 1 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: O 1 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8845 (m-80) REVERT: O 3 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9018 (m-80) REVERT: O 7 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: P 4 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: P 6 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (mtpp) REVERT: P 7 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7853 (t80) REVERT: Q 3 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8924 (m-10) REVERT: Q 6 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8294 (mtmt) REVERT: S 1 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: S 2 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8055 (tmtp) REVERT: S 6 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.4972 (mtmt) REVERT: S 7 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7803 (t80) REVERT: U 7 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8558 (t80) REVERT: V 7 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6326 (m-80) outliers start: 51 outliers final: 23 residues processed: 59 average time/residue: 0.1060 time to fit residues: 6.6724 Evaluate side-chains 62 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 15 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 3 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.089481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080466 restraints weight = 5021.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081740 restraints weight = 3106.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.082631 restraints weight = 2167.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083225 restraints weight = 1637.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.083699 restraints weight = 1338.044| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 1.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.505 1312 Z= 3.517 Angle : 3.923 21.319 1664 Z= 2.031 Chirality : 0.230 0.973 112 Planarity : 0.020 0.063 208 Dihedral : 16.412 52.786 144 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 118.97 Ramachandran Plot: Outliers : 2.08 % Allowed : 66.67 % Favored : 31.25 % Rotamer: Outliers : 45.54 % Allowed : 24.11 % Favored : 30.36 % Cbeta Deviations : 6.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.04 % 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: -10.07 (0.26), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.67 (0.20), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08433 / 3.54 ( 1296) covalent geometry : angle 3.92300 / 2.03 ( 1664) hydrogen bonds : bond 0.40179 / 23.70 ( 27) hydrogen bonds : angle 18.95744 / 11.95 ( 54) Misc. bond : bond 0.00444 / 0.24 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 15 time to evaluate : 0.056 Fit side-chains REVERT: J 1 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8042 (t80) REVERT: J 2 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8396 (tppt) REVERT: J 6 LYS cc_start: 0.9123 (tttm) cc_final: 0.8628 (tppt) REVERT: K 2 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8235 (tppt) REVERT: K 4 GLU cc_start: 0.8054 (tt0) cc_final: 0.7594 (tm-30) REVERT: K 6 LYS cc_start: 0.5003 (OUTLIER) cc_final: 0.2941 (mmtm) REVERT: C 2 LYS cc_start: 0.8908 (tttm) cc_final: 0.8614 (ttmt) REVERT: C 6 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8362 (pttp) REVERT: L 2 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8332 (mmmt) REVERT: L 3 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: L 6 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8926 (mmmt) REVERT: D 3 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: D 4 GLU cc_start: 0.5447 (OUTLIER) cc_final: 0.5184 (pm20) REVERT: D 6 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8568 (pttm) REVERT: M 1 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: O 1 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: O 3 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9087 (m-80) REVERT: O 7 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: P 4 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: P 6 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: P 7 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7935 (t80) REVERT: Q 3 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8934 (m-10) REVERT: Q 5 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8853 (m-10) REVERT: Q 6 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8339 (mtmt) REVERT: S 1 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8701 (m-80) REVERT: S 2 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8128 (tmtp) REVERT: S 4 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: S 6 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5047 (mtmt) REVERT: S 7 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7790 (t80) REVERT: U 7 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8511 (t80) REVERT: V 7 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6324 (m-80) outliers start: 51 outliers final: 23 residues processed: 59 average time/residue: 0.0948 time to fit residues: 6.0147 Evaluate side-chains 64 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 15 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 3 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.088228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079985 restraints weight = 4476.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081171 restraints weight = 2826.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082002 restraints weight = 1994.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.082532 restraints weight = 1550.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082804 restraints weight = 1267.886| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 1.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.506 1312 Z= 3.517 Angle : 3.922 21.507 1664 Z= 2.023 Chirality : 0.230 0.975 112 Planarity : 0.020 0.063 208 Dihedral : 16.522 52.567 144 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 117.74 Ramachandran Plot: Outliers : 2.08 % Allowed : 67.71 % Favored : 30.21 % Rotamer: Outliers : 50.00 % Allowed : 19.64 % Favored : 30.36 % Cbeta Deviations : 6.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.04 % 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: -10.09 (0.26), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.69 (0.20), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08445 / 3.54 ( 1296) covalent geometry : angle 3.92205 / 2.02 ( 1664) hydrogen bonds : bond 0.40392 / 23.72 ( 27) hydrogen bonds : angle 18.99852 / 11.98 ( 54) Misc. bond : bond 0.00437 / 0.24 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 15 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: J 1 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8061 (t80) REVERT: J 2 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8432 (tppt) REVERT: J 6 LYS cc_start: 0.9116 (tttm) cc_final: 0.8662 (tppt) REVERT: K 2 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8310 (tppt) REVERT: K 4 GLU cc_start: 0.8025 (tt0) cc_final: 0.7629 (tm-30) REVERT: K 6 LYS cc_start: 0.5136 (OUTLIER) cc_final: 0.3057 (mmtm) REVERT: C 2 LYS cc_start: 0.8905 (tttm) cc_final: 0.8615 (ttmt) REVERT: C 6 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8402 (pttp) REVERT: L 2 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8375 (mmmt) REVERT: L 3 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: L 6 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8946 (mmmt) REVERT: D 3 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: D 4 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5195 (pm20) REVERT: D 5 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: D 6 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8604 (pttm) REVERT: M 1 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: O 1 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: O 7 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: P 4 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: P 6 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8033 (mtpp) REVERT: P 7 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7941 (t80) REVERT: Q 3 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8948 (m-10) REVERT: Q 5 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8817 (m-10) REVERT: Q 6 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8361 (mtmt) REVERT: S 1 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8715 (m-80) REVERT: S 2 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8189 (tmtp) REVERT: S 4 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: S 6 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5140 (mtmt) REVERT: S 7 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7785 (t80) REVERT: U 7 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8424 (t80) REVERT: V 1 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: V 7 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6420 (m-80) outliers start: 56 outliers final: 25 residues processed: 64 average time/residue: 0.0921 time to fit residues: 6.3255 Evaluate side-chains 67 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 15 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain V residue 1 PHE Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.088532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079941 restraints weight = 5239.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081274 restraints weight = 3148.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082215 restraints weight = 2150.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082840 restraints weight = 1598.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083329 restraints weight = 1267.958| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 1.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.503 1312 Z= 3.510 Angle : 3.934 21.369 1664 Z= 2.025 Chirality : 0.229 0.970 112 Planarity : 0.020 0.063 208 Dihedral : 16.766 52.668 144 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 118.56 Ramachandran Plot: Outliers : 2.08 % Allowed : 68.75 % Favored : 29.17 % Rotamer: Outliers : 50.89 % Allowed : 19.64 % Favored : 29.46 % Cbeta Deviations : 4.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.93 % 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: -10.12 (0.26), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.71 (0.20), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.132 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08428 / 3.53 ( 1296) covalent geometry : angle 3.93395 / 2.03 ( 1664) hydrogen bonds : bond 0.40626 / 23.86 ( 27) hydrogen bonds : angle 18.95966 / 11.94 ( 54) Misc. bond : bond 0.00436 / 0.24 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 15 time to evaluate : 0.055 Fit side-chains revert: symmetry clash REVERT: J 1 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8069 (t80) REVERT: J 2 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8439 (tppt) REVERT: J 6 LYS cc_start: 0.9110 (tttm) cc_final: 0.8676 (tppt) REVERT: K 2 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8311 (tppt) REVERT: K 4 GLU cc_start: 0.8030 (tt0) cc_final: 0.7621 (tm-30) REVERT: K 6 LYS cc_start: 0.5139 (OUTLIER) cc_final: 0.3063 (mmtm) REVERT: C 2 LYS cc_start: 0.8895 (tttm) cc_final: 0.8611 (ttmt) REVERT: C 6 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8410 (pttp) REVERT: L 2 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8375 (mmmt) REVERT: L 3 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: L 6 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8955 (mmmt) REVERT: D 3 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: D 4 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.5009 (pm20) REVERT: D 6 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8618 (pttm) REVERT: M 1 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8129 (m-80) REVERT: O 1 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8893 (m-80) REVERT: O 7 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: P 4 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: P 6 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8043 (mtpp) REVERT: P 7 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7912 (t80) REVERT: Q 3 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8946 (m-10) REVERT: Q 5 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8832 (m-10) REVERT: Q 6 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8360 (mtmt) REVERT: S 1 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: S 2 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8232 (tmtp) REVERT: S 4 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: S 6 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5143 (mtmt) REVERT: S 7 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7796 (t80) REVERT: U 7 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8397 (t80) REVERT: V 1 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: V 7 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6431 (m-80) outliers start: 57 outliers final: 24 residues processed: 65 average time/residue: 0.0876 time to fit residues: 6.1246 Evaluate side-chains 65 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 15 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain V residue 1 PHE Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.088921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.080605 restraints weight = 5431.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081931 restraints weight = 3235.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082875 restraints weight = 2194.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083506 restraints weight = 1612.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084002 restraints weight = 1265.577| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 1.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.503 1312 Z= 3.512 Angle : 3.932 21.414 1664 Z= 2.019 Chirality : 0.229 0.971 112 Planarity : 0.020 0.064 208 Dihedral : 17.116 52.502 144 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 117.33 Ramachandran Plot: Outliers : 3.12 % Allowed : 64.58 % Favored : 32.29 % Rotamer: Outliers : 51.79 % Allowed : 18.75 % Favored : 29.46 % Cbeta Deviations : 4.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.71 % 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: -10.10 (0.25), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.70 (0.19), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.132 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08441 / 3.53 ( 1296) covalent geometry : angle 3.93177 / 2.02 ( 1664) hydrogen bonds : bond 0.40905 / 23.97 ( 27) hydrogen bonds : angle 18.91963 / 11.94 ( 54) Misc. bond : bond 0.00433 / 0.24 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 15 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: J 1 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8080 (t80) REVERT: J 2 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8470 (tppt) REVERT: J 6 LYS cc_start: 0.9096 (tttm) cc_final: 0.8703 (tppt) REVERT: K 2 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8352 (tppt) REVERT: K 4 GLU cc_start: 0.7956 (tt0) cc_final: 0.7662 (tm-30) REVERT: K 6 LYS cc_start: 0.5237 (OUTLIER) cc_final: 0.3142 (mmtm) REVERT: C 2 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8631 (ttmt) REVERT: C 6 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8424 (pttp) REVERT: L 2 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8417 (tppt) REVERT: L 3 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8262 (m-10) REVERT: D 3 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: D 4 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.5212 (pm20) REVERT: D 6 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8643 (pttm) REVERT: M 1 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: O 1 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: O 7 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: P 4 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: P 6 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8067 (mtpp) REVERT: P 7 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7916 (t80) REVERT: Q 3 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8943 (m-10) REVERT: Q 5 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8845 (m-10) REVERT: Q 6 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8388 (mtmt) REVERT: S 1 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: S 2 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8309 (tmtp) REVERT: S 4 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: S 6 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5193 (mtmt) REVERT: S 7 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7812 (t80) REVERT: U 7 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8329 (t80) REVERT: V 1 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: V 7 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6422 (m-80) outliers start: 58 outliers final: 26 residues processed: 65 average time/residue: 0.0933 time to fit residues: 6.4932 Evaluate side-chains 67 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 15 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain V residue 1 PHE Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.089754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081887 restraints weight = 5431.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083156 restraints weight = 3150.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.084093 restraints weight = 2132.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084746 restraints weight = 1553.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084966 restraints weight = 1226.665| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 1.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.504 1312 Z= 3.513 Angle : 3.962 21.403 1664 Z= 2.027 Chirality : 0.231 0.971 112 Planarity : 0.020 0.064 208 Dihedral : 17.513 52.498 144 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 117.33 Ramachandran Plot: Outliers : 3.12 % Allowed : 63.54 % Favored : 33.33 % Rotamer: Outliers : 49.11 % Allowed : 20.54 % Favored : 30.36 % Cbeta Deviations : 4.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 11.61 % 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: -10.08 (0.26), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.68 (0.20), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.133 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08447 / 3.53 ( 1296) covalent geometry : angle 3.96167 / 2.03 ( 1664) hydrogen bonds : bond 0.40918 / 23.98 ( 27) hydrogen bonds : angle 18.94863 / 11.94 ( 54) Misc. bond : bond 0.00437 / 0.24 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 15 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 1 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8078 (t80) REVERT: J 2 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8469 (tppt) REVERT: J 6 LYS cc_start: 0.9087 (tttm) cc_final: 0.8699 (tppt) REVERT: K 2 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8355 (tppt) REVERT: K 4 GLU cc_start: 0.7965 (tt0) cc_final: 0.7661 (tm-30) REVERT: K 6 LYS cc_start: 0.5227 (OUTLIER) cc_final: 0.3144 (mmtm) REVERT: C 2 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8637 (ttmt) REVERT: C 6 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8396 (pttp) REVERT: L 2 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8395 (tppt) REVERT: L 3 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: D 3 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: D 4 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5212 (pm20) REVERT: D 6 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8699 (pttm) REVERT: M 1 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: O 1 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8894 (m-80) REVERT: O 7 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: P 4 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: P 6 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8042 (mtpp) REVERT: P 7 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7958 (t80) REVERT: Q 3 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8939 (m-10) REVERT: Q 5 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8824 (m-10) REVERT: Q 6 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8393 (mtmt) REVERT: S 1 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8748 (m-80) REVERT: S 6 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.5173 (mtmt) REVERT: S 7 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7818 (t80) REVERT: U 7 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8339 (t80) REVERT: V 1 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: V 7 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6446 (m-80) outliers start: 55 outliers final: 26 residues processed: 63 average time/residue: 0.0914 time to fit residues: 6.1812 Evaluate side-chains 65 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 15 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain V residue 1 PHE Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.091982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083794 restraints weight = 6017.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085163 restraints weight = 3450.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086068 restraints weight = 2340.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086684 restraints weight = 1729.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087114 restraints weight = 1324.866| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 1.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.503 1312 Z= 3.518 Angle : 3.967 21.412 1664 Z= 2.032 Chirality : 0.229 0.971 112 Planarity : 0.020 0.064 208 Dihedral : 17.686 52.475 144 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 116.52 Ramachandran Plot: Outliers : 3.12 % Allowed : 63.54 % Favored : 33.33 % Rotamer: Outliers : 47.32 % Allowed : 22.32 % Favored : 30.36 % Cbeta Deviations : 5.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 11.61 % 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: -10.09 (0.26), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.68 (0.20), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.133 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08463 / 3.54 ( 1296) covalent geometry : angle 3.96667 / 2.03 ( 1664) hydrogen bonds : bond 0.40867 / 23.93 ( 27) hydrogen bonds : angle 18.93997 / 11.94 ( 54) Misc. bond : bond 0.00436 / 0.24 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 14 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: J 1 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8089 (t80) REVERT: J 2 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8484 (tppt) REVERT: J 6 LYS cc_start: 0.9079 (tttm) cc_final: 0.8701 (tppt) REVERT: B 6 LYS cc_start: 0.4892 (OUTLIER) cc_final: 0.3453 (pttm) REVERT: K 2 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8369 (tppt) REVERT: K 4 GLU cc_start: 0.7949 (tt0) cc_final: 0.7660 (tm-30) REVERT: K 6 LYS cc_start: 0.5227 (OUTLIER) cc_final: 0.3148 (mmtm) REVERT: C 2 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8671 (ttmt) REVERT: C 6 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8392 (pttp) REVERT: L 2 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8431 (tppt) REVERT: L 3 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8222 (m-10) REVERT: D 3 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: D 4 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.5251 (pm20) REVERT: D 6 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8720 (pttm) REVERT: M 1 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: O 1 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: O 7 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: P 4 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: P 6 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8049 (mtpp) REVERT: P 7 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7955 (t80) REVERT: Q 3 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8937 (m-10) REVERT: Q 5 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8824 (m-10) REVERT: Q 6 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8382 (mtmt) REVERT: S 1 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: S 2 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8318 (tmtp) REVERT: S 6 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5229 (mtmt) REVERT: S 7 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7847 (t80) REVERT: U 7 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8287 (t80) REVERT: V 1 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: V 7 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6433 (m-80) outliers start: 53 outliers final: 25 residues processed: 60 average time/residue: 0.0898 time to fit residues: 5.7696 Evaluate side-chains 65 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 14 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 3 PHE Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 3 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 3 PHE Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain V residue 1 PHE Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 7 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.091987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084473 restraints weight = 4647.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085605 restraints weight = 2845.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086348 restraints weight = 1963.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086940 restraints weight = 1484.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087349 restraints weight = 1176.837| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 1.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.503 1312 Z= 3.517 Angle : 3.960 21.414 1664 Z= 2.029 Chirality : 0.229 0.970 112 Planarity : 0.020 0.064 208 Dihedral : 17.783 53.091 144 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 114.88 Ramachandran Plot: Outliers : 3.12 % Allowed : 63.54 % Favored : 33.33 % Rotamer: Outliers : 46.43 % Allowed : 23.21 % Favored : 30.36 % Cbeta Deviations : 5.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 11.61 % 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: -10.08 (0.26), residues: 96 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.68 (0.20), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.133 0.016 PHE Q 1 Details of bonding type rmsd/Z covalent geometry : bond 0.08458 / 3.54 ( 1296) covalent geometry : angle 3.95958 / 2.03 ( 1664) hydrogen bonds : bond 0.41004 / 23.98 ( 27) hydrogen bonds : angle 18.92797 / 11.93 ( 54) Misc. bond : bond 0.00438 / 0.24 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 339.88 seconds wall clock time: 6 minutes 48.11 seconds (408.11 seconds total)