Starting phenix.real_space_refine on Tue Feb 3 12:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xbm_66705/02_2026/9xbm_66705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xbm_66705/02_2026/9xbm_66705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xbm_66705/02_2026/9xbm_66705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xbm_66705/02_2026/9xbm_66705.map" model { file = "/net/cci-nas-00/data/ceres_data/9xbm_66705/02_2026/9xbm_66705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xbm_66705/02_2026/9xbm_66705.cif" } resolution = 2.4 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 ------------------------------------------------------------------------------- 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= 0.004 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 5 5.16 5 C 1655 2.51 5 N 495 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 2685 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 537 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.45, per 1000 atoms: 0.17 Number of scatterers: 2685 At special positions: 0 Unit cell: (79.68, 62.25, 46.48, 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 5 16.00 O 530 8.00 N 495 7.00 C 1655 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: 0.19 Conformation dependent library (CDL) restraints added in 90.0 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 550 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 52.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 70 through 73 removed outlier: 6.423A pdb=" N GLN B 70 " --> pdb=" O GLN D 71 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR D 73 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 72 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.347A pdb=" N TYR B 79 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR D 82 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 81 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 79 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR B 82 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN A 81 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 85 through 87 removed outlier: 6.472A pdb=" N GLN B 85 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 98 through 114 removed outlier: 8.560A pdb=" N GLY B 99 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LYS D 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N TYR B 101 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N PHE D 104 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN B 103 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR D 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN B 105 " --> pdb=" O TYR D 106 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN D 108 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASN B 107 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU D 110 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 109 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLY D 112 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN B 111 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLN D 114 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 113 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N GLY A 99 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N LYS B 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N TYR A 101 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N PHE B 104 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 103 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR B 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN A 105 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASN B 108 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASN A 107 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU B 110 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASN A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY B 112 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN A 111 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLN B 114 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR A 113 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY C 99 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN A 100 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR C 101 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS A 102 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN C 103 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY E 99 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN C 100 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR E 101 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LYS C 102 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN E 103 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 122 through 132 removed outlier: 6.936A pdb=" N GLY D 123 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE D 129 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN B 130 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 123 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 129 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN A 130 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY A 123 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU C 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 125 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASP C 128 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ASN A 127 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLN C 130 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N PHE A 129 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLN C 132 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS A 131 " --> pdb=" O GLN C 132 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY C 123 " --> pdb=" O MET E 124 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU E 126 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER C 125 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASP E 128 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASN C 127 " --> pdb=" O ASP E 128 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N GLN E 130 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N PHE C 129 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N GLN E 132 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS C 131 " --> pdb=" O GLN E 132 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 171 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: 0.33 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 960 1.34 - 1.46: 563 1.46 - 1.57: 1227 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 2760 Sorted by residual: bond pdb=" CB GLN E 72 " pdb=" CG GLN E 72 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 4.03e-01 bond pdb=" CB GLN D 72 " pdb=" CG GLN D 72 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 3.91e-01 bond pdb=" CB GLN B 72 " pdb=" CG GLN B 72 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 3.80e-01 bond pdb=" CB GLN A 72 " pdb=" CG GLN A 72 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.70e-01 bond pdb=" CB GLN C 72 " pdb=" CG GLN C 72 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.59e-01 ... (remaining 2755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 3156 0.87 - 1.75: 405 1.75 - 2.62: 104 2.62 - 3.49: 25 3.49 - 4.37: 25 Bond angle restraints: 3715 Sorted by residual: angle pdb=" N GLN A 118 " pdb=" CA GLN A 118 " pdb=" C GLN A 118 " ideal model delta sigma weight residual 108.76 111.86 -3.10 1.44e+00 4.82e-01 4.64e+00 angle pdb=" N GLN B 118 " pdb=" CA GLN B 118 " pdb=" C GLN B 118 " ideal model delta sigma weight residual 108.76 111.85 -3.09 1.44e+00 4.82e-01 4.61e+00 angle pdb=" N GLN D 118 " pdb=" CA GLN D 118 " pdb=" C GLN D 118 " ideal model delta sigma weight residual 108.76 111.83 -3.07 1.44e+00 4.82e-01 4.56e+00 angle pdb=" N GLN E 118 " pdb=" CA GLN E 118 " pdb=" C GLN E 118 " ideal model delta sigma weight residual 108.76 111.83 -3.07 1.44e+00 4.82e-01 4.56e+00 angle pdb=" N GLN C 118 " pdb=" CA GLN C 118 " pdb=" C GLN C 118 " ideal model delta sigma weight residual 108.76 111.82 -3.06 1.44e+00 4.82e-01 4.52e+00 ... (remaining 3710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 1425 16.45 - 32.90: 100 32.90 - 49.35: 40 49.35 - 65.80: 20 65.80 - 82.25: 10 Dihedral angle restraints: 1595 sinusoidal: 685 harmonic: 910 Sorted by residual: dihedral pdb=" CA TYR E 113 " pdb=" C TYR E 113 " pdb=" N GLN E 114 " pdb=" CA GLN E 114 " ideal model delta harmonic sigma weight residual 180.00 165.14 14.86 0 5.00e+00 4.00e-02 8.83e+00 dihedral pdb=" CA TYR C 113 " pdb=" C TYR C 113 " pdb=" N GLN C 114 " pdb=" CA GLN C 114 " ideal model delta harmonic sigma weight residual 180.00 165.15 14.85 0 5.00e+00 4.00e-02 8.82e+00 dihedral pdb=" CA TYR B 113 " pdb=" C TYR B 113 " pdb=" N GLN B 114 " pdb=" CA GLN B 114 " ideal model delta harmonic sigma weight residual 180.00 165.15 14.85 0 5.00e+00 4.00e-02 8.82e+00 ... (remaining 1592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 137 0.023 - 0.046: 89 0.046 - 0.070: 49 0.070 - 0.093: 0 0.093 - 0.116: 10 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA PHE D 117 " pdb=" N PHE D 117 " pdb=" C PHE D 117 " pdb=" CB PHE D 117 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.36e-01 chirality pdb=" CA PHE A 117 " pdb=" N PHE A 117 " pdb=" C PHE A 117 " pdb=" CB PHE A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA PHE B 117 " pdb=" N PHE B 117 " pdb=" C PHE B 117 " pdb=" CB PHE B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.62 -0.11 2.00e-01 2.50e+01 3.16e-01 ... (remaining 282 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 103 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ASN A 103 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN A 103 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 104 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 103 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ASN B 103 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN B 103 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 104 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 103 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C ASN E 103 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN E 103 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE E 104 " -0.013 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1307 2.96 - 3.45: 2446 3.45 - 3.93: 4909 3.93 - 4.42: 5710 4.42 - 4.90: 9501 Nonbonded interactions: 23873 Sorted by model distance: nonbonded pdb=" O TYR E 73 " pdb=" ND2 ASN E 74 " model vdw 2.480 3.120 nonbonded pdb=" O TYR D 73 " pdb=" ND2 ASN D 74 " model vdw 2.480 3.120 nonbonded pdb=" O TYR C 73 " pdb=" ND2 ASN C 74 " model vdw 2.481 3.120 nonbonded pdb=" O TYR A 73 " pdb=" ND2 ASN A 74 " model vdw 2.481 3.120 nonbonded pdb=" O TYR B 73 " pdb=" ND2 ASN B 74 " model vdw 2.481 3.120 ... (remaining 23868 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.530 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.120 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 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 : 0.004 0.022 2760 Z= 0.181 Angle : 0.740 4.367 3715 Z= 0.405 Chirality : 0.038 0.116 285 Planarity : 0.006 0.022 555 Dihedral : 16.597 82.253 1045 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -4.35 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 98 TYR 0.017 0.002 TYR E 113 PHE 0.014 0.003 PHE A 117 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 2760) covalent geometry : angle 0.73961 ( 3715) hydrogen bonds : bond 0.14920 ( 57) hydrogen bonds : angle 10.93337 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.5786 time to fit residues: 20.7564 Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 74 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN B 72 GLN B 74 ASN B 81 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 72 GLN C 74 ASN C 81 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN D 74 ASN D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN E 72 GLN E 74 ASN E 81 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097519 restraints weight = 2629.027| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.52 r_work: 0.3325 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2760 Z= 0.163 Angle : 0.678 5.013 3715 Z= 0.368 Chirality : 0.037 0.100 285 Planarity : 0.003 0.024 555 Dihedral : 4.749 16.363 365 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.37 % Allowed : 6.30 % Favored : 93.33 % 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: -4.20 (0.22), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.17), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.015 0.002 TYR A 79 PHE 0.012 0.002 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2760) covalent geometry : angle 0.67844 ( 3715) hydrogen bonds : bond 0.04755 ( 57) hydrogen bonds : angle 7.62383 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.104 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.3610 time to fit residues: 14.1282 Evaluate side-chains 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.114703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095777 restraints weight = 2665.116| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.52 r_work: 0.3295 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2760 Z= 0.225 Angle : 0.724 5.767 3715 Z= 0.391 Chirality : 0.037 0.108 285 Planarity : 0.003 0.026 555 Dihedral : 4.854 16.210 365 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -3.98 (0.23), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.014 0.002 TYR B 82 PHE 0.013 0.003 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 2760) covalent geometry : angle 0.72394 ( 3715) hydrogen bonds : bond 0.05147 ( 57) hydrogen bonds : angle 7.28055 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.105 Fit side-chains REVERT: C 128 ASP cc_start: 0.8134 (t0) cc_final: 0.7772 (t70) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.4123 time to fit residues: 14.8433 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.116075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097188 restraints weight = 2631.339| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.51 r_work: 0.3320 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2760 Z= 0.165 Angle : 0.672 5.309 3715 Z= 0.359 Chirality : 0.035 0.092 285 Planarity : 0.003 0.026 555 Dihedral : 4.737 15.670 365 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.37 % Allowed : 7.41 % Favored : 92.22 % 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: -3.93 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 98 TYR 0.015 0.002 TYR A 79 PHE 0.011 0.002 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2760) covalent geometry : angle 0.67225 ( 3715) hydrogen bonds : bond 0.04454 ( 57) hydrogen bonds : angle 6.86340 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.108 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.4919 time to fit residues: 17.1815 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 0.0020 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 overall best weight: 4.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097691 restraints weight = 2630.993| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.51 r_work: 0.3313 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2760 Z= 0.190 Angle : 0.693 5.047 3715 Z= 0.372 Chirality : 0.036 0.097 285 Planarity : 0.003 0.026 555 Dihedral : 4.771 15.685 365 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % 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: -3.89 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.013 0.002 TYR E 79 PHE 0.011 0.002 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 2760) covalent geometry : angle 0.69301 ( 3715) hydrogen bonds : bond 0.04704 ( 57) hydrogen bonds : angle 6.87402 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.5457 time to fit residues: 19.6359 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.117298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.098644 restraints weight = 2646.221| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.51 r_work: 0.3337 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2760 Z= 0.153 Angle : 0.660 5.459 3715 Z= 0.352 Chirality : 0.035 0.090 285 Planarity : 0.003 0.025 555 Dihedral : 4.682 15.256 365 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.48 % Allowed : 7.41 % Favored : 91.11 % 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: -3.88 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 98 TYR 0.014 0.002 TYR E 79 PHE 0.010 0.002 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 2760) covalent geometry : angle 0.66018 ( 3715) hydrogen bonds : bond 0.04182 ( 57) hydrogen bonds : angle 6.65742 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.108 Fit side-chains REVERT: E 69 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.6382 (m-80) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.4679 time to fit residues: 16.8410 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain E residue 69 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.115600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096916 restraints weight = 2642.350| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.51 r_work: 0.3303 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2760 Z= 0.219 Angle : 0.725 5.797 3715 Z= 0.389 Chirality : 0.036 0.105 285 Planarity : 0.003 0.025 555 Dihedral : 4.809 15.889 365 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.74 % Allowed : 8.89 % Favored : 90.37 % 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: -3.88 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.018 0.002 TYR A 79 PHE 0.011 0.002 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 2760) covalent geometry : angle 0.72502 ( 3715) hydrogen bonds : bond 0.04940 ( 57) hydrogen bonds : angle 6.87119 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.063 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.3358 time to fit residues: 12.4617 Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097958 restraints weight = 2689.870| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.50 r_work: 0.3334 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2760 Z= 0.184 Angle : 0.692 5.344 3715 Z= 0.370 Chirality : 0.035 0.096 285 Planarity : 0.003 0.025 555 Dihedral : 4.754 15.550 365 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % 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: -3.89 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.018 0.002 TYR A 79 PHE 0.010 0.002 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2760) covalent geometry : angle 0.69170 ( 3715) hydrogen bonds : bond 0.04450 ( 57) hydrogen bonds : angle 6.73780 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.063 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.3904 time to fit residues: 13.2733 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.0020 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.115688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097441 restraints weight = 2739.728| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.53 r_work: 0.3323 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2760 Z= 0.200 Angle : 0.718 5.912 3715 Z= 0.385 Chirality : 0.036 0.100 285 Planarity : 0.003 0.024 555 Dihedral : 4.791 15.781 365 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.020 0.002 TYR C 79 PHE 0.011 0.002 PHE D 117 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 2760) covalent geometry : angle 0.71783 ( 3715) hydrogen bonds : bond 0.04729 ( 57) hydrogen bonds : angle 6.84609 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.065 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.4896 time to fit residues: 15.6376 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098794 restraints weight = 2700.192| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.52 r_work: 0.3350 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2760 Z= 0.151 Angle : 0.673 5.620 3715 Z= 0.359 Chirality : 0.035 0.087 285 Planarity : 0.003 0.024 555 Dihedral : 4.683 15.258 365 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.18), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.019 0.002 TYR E 79 PHE 0.010 0.002 PHE B 129 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 2760) covalent geometry : angle 0.67334 ( 3715) hydrogen bonds : bond 0.04060 ( 57) hydrogen bonds : angle 6.61440 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.064 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.4028 time to fit residues: 12.8944 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.0050 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.117145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099113 restraints weight = 2675.500| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.50 r_work: 0.3360 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2760 Z= 0.141 Angle : 0.660 5.451 3715 Z= 0.352 Chirality : 0.034 0.084 285 Planarity : 0.003 0.023 555 Dihedral : 4.634 15.059 365 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.24), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 98 TYR 0.018 0.002 TYR E 79 PHE 0.009 0.002 PHE C 117 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2760) covalent geometry : angle 0.65991 ( 3715) hydrogen bonds : bond 0.03901 ( 57) hydrogen bonds : angle 6.54653 ( 171) =============================================================================== Job complete usr+sys time: 1005.47 seconds wall clock time: 17 minutes 50.50 seconds (1070.50 seconds total)