Starting phenix.real_space_refine on Tue Feb 3 12:19:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhh_61482/02_2026/9jhh_61482.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhh_61482/02_2026/9jhh_61482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhh_61482/02_2026/9jhh_61482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhh_61482/02_2026/9jhh_61482.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhh_61482/02_2026/9jhh_61482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhh_61482/02_2026/9jhh_61482.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 930 2.51 5 N 222 2.21 5 O 270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1434 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "E" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Time building chain proxies: 0.42, per 1000 atoms: 0.29 Number of scatterers: 1434 At special positions: 0 Unit cell: (83, 48.14, 34.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 270 8.00 N 222 7.00 C 930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.10 Conformation dependent library (CDL) restraints added in 55.2 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 54.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 13 removed outlier: 7.023A pdb=" N VAL B 3 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 4 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN B 5 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 6 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N MET B 7 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS A 8 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 9 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N VAL A 3 " --> pdb=" O THR C 4 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N THR C 6 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLN A 5 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N LYS C 8 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N MET A 7 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N LEU C 10 " --> pdb=" O MET A 7 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY A 9 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE C 12 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP A 11 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 31 removed outlier: 6.232A pdb=" N ALA A 23 " --> pdb=" O MET B 24 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA B 26 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 25 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER A 27 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N SER B 30 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ILE A 29 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 27 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A 28 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 29 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER A 30 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU C 31 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 2 through 13 removed outlier: 7.114A pdb=" N VAL E 3 " --> pdb=" O ILE D 2 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR D 4 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN E 5 " --> pdb=" O THR D 4 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR D 6 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET E 7 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS D 8 " --> pdb=" O MET E 7 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY E 9 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N VAL D 3 " --> pdb=" O THR F 4 " (cutoff:3.500A) removed outlier: 9.825A pdb=" N THR F 6 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLN D 5 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N LYS F 8 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N MET D 7 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LEU F 10 " --> pdb=" O MET D 7 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY D 9 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE F 12 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP D 11 " --> pdb=" O ILE F 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 25 removed outlier: 6.083A pdb=" N ALA D 23 " --> pdb=" O MET E 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.645A pdb=" N ASP D 28 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N LEU E 31 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER D 30 " --> pdb=" O LEU E 31 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 48 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: 0.15 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 426 1.34 - 1.46: 249 1.46 - 1.57: 747 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 1446 Sorted by residual: bond pdb=" N ILE C 29 " pdb=" CA ILE C 29 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.19e-02 7.06e+03 8.87e+00 bond pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.19e-02 7.06e+03 8.81e+00 bond pdb=" N ILE A 29 " pdb=" CA ILE A 29 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.71e+00 bond pdb=" N VAL C 15 " pdb=" CA VAL C 15 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N ILE F 29 " pdb=" CA ILE F 29 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.22e-02 6.72e+03 8.15e+00 ... (remaining 1441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 1289 0.75 - 1.51: 433 1.51 - 2.26: 141 2.26 - 3.02: 63 3.02 - 3.77: 30 Bond angle restraints: 1956 Sorted by residual: angle pdb=" CA LYS D 14 " pdb=" C LYS D 14 " pdb=" O LYS D 14 " ideal model delta sigma weight residual 121.84 118.11 3.73 1.16e+00 7.43e-01 1.04e+01 angle pdb=" CA THR C 18 " pdb=" C THR C 18 " pdb=" O THR C 18 " ideal model delta sigma weight residual 121.78 118.19 3.59 1.12e+00 7.97e-01 1.03e+01 angle pdb=" CA LYS F 14 " pdb=" C LYS F 14 " pdb=" O LYS F 14 " ideal model delta sigma weight residual 121.84 118.13 3.71 1.16e+00 7.43e-01 1.02e+01 angle pdb=" CA LYS E 14 " pdb=" C LYS E 14 " pdb=" O LYS E 14 " ideal model delta sigma weight residual 121.84 118.13 3.71 1.16e+00 7.43e-01 1.02e+01 angle pdb=" CA THR A 18 " pdb=" C THR A 18 " pdb=" O THR A 18 " ideal model delta sigma weight residual 121.78 118.22 3.56 1.12e+00 7.97e-01 1.01e+01 ... (remaining 1951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.16: 696 10.16 - 20.33: 84 20.33 - 30.49: 57 30.49 - 40.66: 12 40.66 - 50.82: 15 Dihedral angle restraints: 864 sinusoidal: 312 harmonic: 552 Sorted by residual: dihedral pdb=" CA ILE F 12 " pdb=" CB ILE F 12 " pdb=" CG1 ILE F 12 " pdb=" CD1 ILE F 12 " ideal model delta sinusoidal sigma weight residual 180.00 129.18 50.82 3 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CA ILE D 12 " pdb=" CB ILE D 12 " pdb=" CG1 ILE D 12 " pdb=" CD1 ILE D 12 " ideal model delta sinusoidal sigma weight residual 180.00 129.21 50.79 3 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CA ILE E 12 " pdb=" CB ILE E 12 " pdb=" CG1 ILE E 12 " pdb=" CD1 ILE E 12 " ideal model delta sinusoidal sigma weight residual 180.00 129.21 50.79 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 861 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.039: 151 0.039 - 0.077: 29 0.077 - 0.116: 49 0.116 - 0.154: 21 0.154 - 0.192: 8 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA ILE C 29 " pdb=" N ILE C 29 " pdb=" C ILE C 29 " pdb=" CB ILE C 29 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA ILE A 29 " pdb=" N ILE A 29 " pdb=" C ILE A 29 " pdb=" CB ILE A 29 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 255 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 10 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.06e+00 pdb=" C LEU B 10 " 0.018 2.00e-02 2.50e+03 pdb=" O LEU B 10 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP B 11 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 10 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.03e+00 pdb=" C LEU A 10 " 0.018 2.00e-02 2.50e+03 pdb=" O LEU A 10 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP A 11 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 10 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C LEU C 10 " -0.018 2.00e-02 2.50e+03 pdb=" O LEU C 10 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP C 11 " 0.006 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 674 2.93 - 3.43: 1271 3.43 - 3.92: 2337 3.92 - 4.41: 2212 4.41 - 4.90: 4782 Nonbonded interactions: 11276 Sorted by model distance: nonbonded pdb=" CD2 LEU D 31 " pdb=" CE2 TYR F 20 " model vdw 2.443 3.760 nonbonded pdb=" CE2 TYR D 20 " pdb=" CD2 LEU E 31 " model vdw 2.455 3.760 nonbonded pdb=" O VAL C 15 " pdb=" CG1 VAL C 15 " model vdw 2.507 3.460 nonbonded pdb=" O VAL D 15 " pdb=" CG1 VAL D 15 " model vdw 2.507 3.460 nonbonded pdb=" O VAL B 15 " pdb=" CG1 VAL B 15 " model vdw 2.507 3.460 ... (remaining 11271 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.150 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.011 0.036 1446 Z= 0.707 Angle : 0.990 3.772 1956 Z= 0.668 Chirality : 0.070 0.192 258 Planarity : 0.003 0.010 222 Dihedral : 14.509 50.823 504 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 43.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 13.46 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.53), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR A 20 TRP 0.009 0.003 TRP C 19 Details of bonding type rmsd covalent geometry : bond 0.01102 ( 1446) covalent geometry : angle 0.99003 ( 1956) hydrogen bonds : bond 0.17744 ( 16) hydrogen bonds : angle 7.74741 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8256 (mt) cc_final: 0.8021 (mt) REVERT: A 30 SER cc_start: 0.8070 (m) cc_final: 0.7751 (t) REVERT: C 30 SER cc_start: 0.8218 (m) cc_final: 0.7791 (t) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0290 time to fit residues: 1.8130 Evaluate side-chains 47 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.179094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.158762 restraints weight = 1683.251| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 3.40 r_work: 0.4337 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1446 Z= 0.109 Angle : 0.431 2.447 1956 Z= 0.231 Chirality : 0.047 0.188 258 Planarity : 0.002 0.006 222 Dihedral : 3.632 11.535 192 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 7.05 % Allowed : 19.87 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.55), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR F 20 TRP 0.010 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 1446) covalent geometry : angle 0.43144 ( 1956) hydrogen bonds : bond 0.01748 ( 16) hydrogen bonds : angle 4.33800 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.033 Fit side-chains REVERT: D 19 TRP cc_start: 0.7872 (t-100) cc_final: 0.7351 (t60) REVERT: E 29 ILE cc_start: 0.8385 (mt) cc_final: 0.8165 (mt) REVERT: C 19 TRP cc_start: 0.8282 (t60) cc_final: 0.8082 (t60) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.0302 time to fit residues: 1.7365 Evaluate side-chains 44 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 0.0020 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.0170 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.1830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.160553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.139432 restraints weight = 1736.809| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 3.22 r_work: 0.4243 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1446 Z= 0.145 Angle : 0.498 3.396 1956 Z= 0.262 Chirality : 0.047 0.187 258 Planarity : 0.002 0.008 222 Dihedral : 3.638 12.080 192 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 7.05 % Allowed : 21.15 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR F 20 TRP 0.015 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 1446) covalent geometry : angle 0.49757 ( 1956) hydrogen bonds : bond 0.01563 ( 16) hydrogen bonds : angle 4.05408 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.054 Fit side-chains REVERT: D 19 TRP cc_start: 0.8154 (t-100) cc_final: 0.7767 (t60) outliers start: 11 outliers final: 8 residues processed: 42 average time/residue: 0.0435 time to fit residues: 2.1664 Evaluate side-chains 38 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.145801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.126915 restraints weight = 1746.571| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 3.08 r_work: 0.4172 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1446 Z= 0.156 Angle : 0.482 3.810 1956 Z= 0.253 Chirality : 0.046 0.199 258 Planarity : 0.002 0.007 222 Dihedral : 3.780 12.505 192 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 7.05 % Allowed : 23.08 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR F 20 TRP 0.014 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 1446) covalent geometry : angle 0.48192 ( 1956) hydrogen bonds : bond 0.01796 ( 16) hydrogen bonds : angle 3.66725 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.057 Fit side-chains REVERT: D 19 TRP cc_start: 0.7950 (t-100) cc_final: 0.7514 (t60) REVERT: F 7 MET cc_start: 0.7414 (mpp) cc_final: 0.7213 (mtm) outliers start: 11 outliers final: 9 residues processed: 39 average time/residue: 0.0396 time to fit residues: 1.8704 Evaluate side-chains 39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.146454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.127744 restraints weight = 1699.348| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 3.02 r_work: 0.4194 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1446 Z= 0.148 Angle : 0.466 3.728 1956 Z= 0.244 Chirality : 0.045 0.163 258 Planarity : 0.002 0.006 222 Dihedral : 3.692 12.465 192 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 7.69 % Allowed : 25.00 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.53), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR F 20 TRP 0.013 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 1446) covalent geometry : angle 0.46632 ( 1956) hydrogen bonds : bond 0.01689 ( 16) hydrogen bonds : angle 3.56172 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.056 Fit side-chains REVERT: D 19 TRP cc_start: 0.7888 (t-100) cc_final: 0.7499 (t60) outliers start: 12 outliers final: 9 residues processed: 41 average time/residue: 0.0381 time to fit residues: 1.8887 Evaluate side-chains 39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.141328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.122483 restraints weight = 1748.849| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 3.05 r_work: 0.4120 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1446 Z= 0.205 Angle : 0.535 3.664 1956 Z= 0.286 Chirality : 0.047 0.158 258 Planarity : 0.002 0.008 222 Dihedral : 4.147 12.834 192 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 7.05 % Allowed : 25.64 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR F 20 TRP 0.017 0.003 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 1446) covalent geometry : angle 0.53519 ( 1956) hydrogen bonds : bond 0.01883 ( 16) hydrogen bonds : angle 3.71955 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.056 Fit side-chains REVERT: D 19 TRP cc_start: 0.7883 (t-100) cc_final: 0.7504 (t60) REVERT: F 7 MET cc_start: 0.7539 (mtm) cc_final: 0.6473 (mtt) REVERT: F 22 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8103 (tt) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.0424 time to fit residues: 2.1156 Evaluate side-chains 42 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.143826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.125001 restraints weight = 1758.967| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 3.09 r_work: 0.4149 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1446 Z= 0.178 Angle : 0.513 4.124 1956 Z= 0.272 Chirality : 0.046 0.157 258 Planarity : 0.002 0.007 222 Dihedral : 3.999 12.075 192 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 7.69 % Allowed : 26.28 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.50), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR F 20 TRP 0.017 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 1446) covalent geometry : angle 0.51263 ( 1956) hydrogen bonds : bond 0.01788 ( 16) hydrogen bonds : angle 3.69740 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.057 Fit side-chains REVERT: D 19 TRP cc_start: 0.7708 (t-100) cc_final: 0.7354 (t60) REVERT: F 7 MET cc_start: 0.7549 (mtm) cc_final: 0.6476 (mtt) REVERT: F 22 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8122 (tt) outliers start: 12 outliers final: 9 residues processed: 41 average time/residue: 0.0449 time to fit residues: 2.1852 Evaluate side-chains 41 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.142279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.123518 restraints weight = 1718.167| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.97 r_work: 0.4122 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1446 Z= 0.201 Angle : 0.531 4.028 1956 Z= 0.283 Chirality : 0.046 0.157 258 Planarity : 0.002 0.007 222 Dihedral : 4.154 12.368 192 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 6.41 % Allowed : 27.56 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.50), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 20 TRP 0.018 0.003 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 1446) covalent geometry : angle 0.53091 ( 1956) hydrogen bonds : bond 0.01895 ( 16) hydrogen bonds : angle 3.88418 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.059 Fit side-chains REVERT: D 19 TRP cc_start: 0.7624 (t-100) cc_final: 0.7374 (t60) REVERT: F 22 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8188 (tt) outliers start: 10 outliers final: 8 residues processed: 39 average time/residue: 0.0443 time to fit residues: 2.0620 Evaluate side-chains 39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.161791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.142611 restraints weight = 1745.062| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 2.96 r_work: 0.4311 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1446 Z= 0.108 Angle : 0.453 4.067 1956 Z= 0.238 Chirality : 0.046 0.169 258 Planarity : 0.002 0.008 222 Dihedral : 3.430 10.698 192 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 5.77 % Allowed : 27.56 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.52), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR F 20 TRP 0.015 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 1446) covalent geometry : angle 0.45341 ( 1956) hydrogen bonds : bond 0.01552 ( 16) hydrogen bonds : angle 3.65604 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.054 Fit side-chains REVERT: D 19 TRP cc_start: 0.7720 (t-100) cc_final: 0.7488 (t60) REVERT: F 7 MET cc_start: 0.7568 (mtm) cc_final: 0.6549 (mtt) REVERT: F 22 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8245 (tt) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.0378 time to fit residues: 1.9657 Evaluate side-chains 42 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.153568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.134786 restraints weight = 1629.860| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.93 r_work: 0.4210 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1446 Z= 0.163 Angle : 0.516 4.164 1956 Z= 0.273 Chirality : 0.046 0.170 258 Planarity : 0.002 0.008 222 Dihedral : 3.747 11.781 192 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 5.77 % Allowed : 28.85 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 20 TRP 0.019 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 1446) covalent geometry : angle 0.51579 ( 1956) hydrogen bonds : bond 0.01705 ( 16) hydrogen bonds : angle 3.74656 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.054 Fit side-chains REVERT: D 19 TRP cc_start: 0.7691 (t-100) cc_final: 0.7373 (t60) REVERT: F 7 MET cc_start: 0.7583 (mtm) cc_final: 0.6530 (mtt) REVERT: F 22 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8189 (tt) outliers start: 9 outliers final: 8 residues processed: 39 average time/residue: 0.0423 time to fit residues: 1.9595 Evaluate side-chains 40 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.160757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.141791 restraints weight = 1814.496| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.96 r_work: 0.4294 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1446 Z= 0.121 Angle : 0.485 4.225 1956 Z= 0.255 Chirality : 0.046 0.169 258 Planarity : 0.002 0.011 222 Dihedral : 3.514 10.946 192 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 6.41 % Allowed : 29.49 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.52), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 20 TRP 0.016 0.002 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 1446) covalent geometry : angle 0.48549 ( 1956) hydrogen bonds : bond 0.01569 ( 16) hydrogen bonds : angle 3.70937 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 544.27 seconds wall clock time: 10 minutes 3.11 seconds (603.11 seconds total)