Starting phenix.real_space_refine on Wed Sep 17 22:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zra_60394/09_2025/8zra_60394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zra_60394/09_2025/8zra_60394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zra_60394/09_2025/8zra_60394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zra_60394/09_2025/8zra_60394.map" model { file = "/net/cci-nas-00/data/ceres_data/8zra_60394/09_2025/8zra_60394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zra_60394/09_2025/8zra_60394.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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 36 5.16 5 C 7614 2.51 5 N 1890 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11772 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 654 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R Time building chain proxies: 1.21, per 1000 atoms: 0.10 Number of scatterers: 11772 At special positions: 0 Unit cell: (97.65, 97.65, 86.1, 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 36 16.00 O 2232 8.00 N 1890 7.00 C 7614 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: 1.05 Conformation dependent library (CDL) restraints added in 383.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 18 sheets defined 21.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 97 " --> pdb=" O ILE A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 97' Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 97 " --> pdb=" O ILE B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 97 " --> pdb=" O ILE C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 93 through 97' Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 154 through 156 No H-bonds generated for 'chain 'C' and resid 154 through 156' Processing helix chain 'D' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 97 " --> pdb=" O ILE D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 97' Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER E 97 " --> pdb=" O ILE E 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 97' Processing helix chain 'E' and resid 98 through 106 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'F' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER F 97 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 97' Processing helix chain 'F' and resid 98 through 106 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'G' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G 97 " --> pdb=" O ILE G 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 93 through 97' Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 154 through 156 No H-bonds generated for 'chain 'G' and resid 154 through 156' Processing helix chain 'H' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU H 96 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER H 97 " --> pdb=" O ILE H 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 97' Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'I' and resid 93 through 97 removed outlier: 3.731A pdb=" N GLU I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER I 97 " --> pdb=" O ILE I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 93 through 97' Processing helix chain 'I' and resid 98 through 106 Processing helix chain 'I' and resid 154 through 156 No H-bonds generated for 'chain 'I' and resid 154 through 156' Processing helix chain 'J' and resid 93 through 97 removed outlier: 3.731A pdb=" N GLU J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER J 97 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 97' Processing helix chain 'J' and resid 98 through 106 Processing helix chain 'J' and resid 154 through 156 No H-bonds generated for 'chain 'J' and resid 154 through 156' Processing helix chain 'K' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU K 96 " --> pdb=" O PRO K 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER K 97 " --> pdb=" O ILE K 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 93 through 97' Processing helix chain 'K' and resid 98 through 106 Processing helix chain 'K' and resid 154 through 156 No H-bonds generated for 'chain 'K' and resid 154 through 156' Processing helix chain 'L' and resid 93 through 97 removed outlier: 3.731A pdb=" N GLU L 96 " --> pdb=" O PRO L 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 97 " --> pdb=" O ILE L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 93 through 97' Processing helix chain 'L' and resid 98 through 106 Processing helix chain 'L' and resid 154 through 156 No H-bonds generated for 'chain 'L' and resid 154 through 156' Processing helix chain 'M' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU M 96 " --> pdb=" O PRO M 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER M 97 " --> pdb=" O ILE M 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 93 through 97' Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 154 through 156 No H-bonds generated for 'chain 'M' and resid 154 through 156' Processing helix chain 'N' and resid 93 through 97 removed outlier: 3.731A pdb=" N GLU N 96 " --> pdb=" O PRO N 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER N 97 " --> pdb=" O ILE N 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 93 through 97' Processing helix chain 'N' and resid 98 through 106 Processing helix chain 'N' and resid 154 through 156 No H-bonds generated for 'chain 'N' and resid 154 through 156' Processing helix chain 'O' and resid 93 through 97 removed outlier: 3.731A pdb=" N GLU O 96 " --> pdb=" O PRO O 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER O 97 " --> pdb=" O ILE O 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 93 through 97' Processing helix chain 'O' and resid 98 through 106 Processing helix chain 'O' and resid 154 through 156 No H-bonds generated for 'chain 'O' and resid 154 through 156' Processing helix chain 'P' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU P 96 " --> pdb=" O PRO P 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER P 97 " --> pdb=" O ILE P 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 93 through 97' Processing helix chain 'P' and resid 98 through 106 Processing helix chain 'P' and resid 154 through 156 No H-bonds generated for 'chain 'P' and resid 154 through 156' Processing helix chain 'Q' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU Q 96 " --> pdb=" O PRO Q 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER Q 97 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 93 through 97' Processing helix chain 'Q' and resid 98 through 106 Processing helix chain 'Q' and resid 154 through 156 No H-bonds generated for 'chain 'Q' and resid 154 through 156' Processing helix chain 'R' and resid 93 through 97 removed outlier: 3.730A pdb=" N GLU R 96 " --> pdb=" O PRO R 93 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER R 97 " --> pdb=" O ILE R 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 93 through 97' Processing helix chain 'R' and resid 98 through 106 Processing helix chain 'R' and resid 154 through 156 No H-bonds generated for 'chain 'R' and resid 154 through 156' Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 143 removed outlier: 7.066A pdb=" N ILE A 141 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE C 141 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE D 141 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE E 141 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE F 141 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE G 141 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE H 141 " --> pdb=" O GLU H 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE J 141 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 140 through 143 removed outlier: 7.066A pdb=" N ILE I 141 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE K 141 " --> pdb=" O GLU K 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 151 through 152 removed outlier: 7.067A pdb=" N ILE L 141 " --> pdb=" O GLU L 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE M 141 " --> pdb=" O GLU M 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE N 141 " --> pdb=" O GLU N 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 151 through 152 removed outlier: 7.067A pdb=" N ILE O 141 " --> pdb=" O GLU O 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE P 141 " --> pdb=" O GLU P 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE Q 141 " --> pdb=" O GLU Q 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 151 through 152 removed outlier: 7.066A pdb=" N ILE R 141 " --> pdb=" O GLU R 133 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1026 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: 1.70 Time building geometry restraints manager: 1.41 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: 3690 1.34 - 1.46: 2456 1.46 - 1.57: 5788 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 12006 Sorted by residual: bond pdb=" N PRO B 93 " pdb=" CA PRO B 93 " ideal model delta sigma weight residual 1.469 1.451 0.018 1.28e-02 6.10e+03 1.95e+00 bond pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 1.469 1.451 0.018 1.28e-02 6.10e+03 1.94e+00 bond pdb=" N PRO G 93 " pdb=" CA PRO G 93 " ideal model delta sigma weight residual 1.469 1.451 0.018 1.28e-02 6.10e+03 1.92e+00 bond pdb=" N PRO F 93 " pdb=" CA PRO F 93 " ideal model delta sigma weight residual 1.469 1.451 0.018 1.28e-02 6.10e+03 1.91e+00 bond pdb=" N PRO E 93 " pdb=" CA PRO E 93 " ideal model delta sigma weight residual 1.469 1.451 0.018 1.28e-02 6.10e+03 1.90e+00 ... (remaining 12001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 14134 0.96 - 1.93: 1517 1.93 - 2.89: 402 2.89 - 3.85: 93 3.85 - 4.82: 90 Bond angle restraints: 16236 Sorted by residual: angle pdb=" C ASP F 159 " pdb=" N TYR F 160 " pdb=" CA TYR F 160 " ideal model delta sigma weight residual 121.63 116.90 4.73 1.92e+00 2.71e-01 6.07e+00 angle pdb=" C ASP O 159 " pdb=" N TYR O 160 " pdb=" CA TYR O 160 " ideal model delta sigma weight residual 121.63 116.91 4.72 1.92e+00 2.71e-01 6.04e+00 angle pdb=" C ASP R 159 " pdb=" N TYR R 160 " pdb=" CA TYR R 160 " ideal model delta sigma weight residual 121.63 116.91 4.72 1.92e+00 2.71e-01 6.04e+00 angle pdb=" C ASP K 159 " pdb=" N TYR K 160 " pdb=" CA TYR K 160 " ideal model delta sigma weight residual 121.63 116.92 4.71 1.92e+00 2.71e-01 6.02e+00 angle pdb=" C ASP N 159 " pdb=" N TYR N 160 " pdb=" CA TYR N 160 " ideal model delta sigma weight residual 121.63 116.93 4.70 1.92e+00 2.71e-01 6.00e+00 ... (remaining 16231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 5958 14.34 - 28.67: 864 28.67 - 43.01: 270 43.01 - 57.34: 72 57.34 - 71.68: 18 Dihedral angle restraints: 7182 sinusoidal: 2970 harmonic: 4212 Sorted by residual: dihedral pdb=" CA PHE I 117 " pdb=" C PHE I 117 " pdb=" N GLU I 118 " pdb=" CA GLU I 118 " ideal model delta harmonic sigma weight residual 180.00 -163.26 -16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE J 117 " pdb=" C PHE J 117 " pdb=" N GLU J 118 " pdb=" CA GLU J 118 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE G 117 " pdb=" C PHE G 117 " pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1063 0.035 - 0.070: 439 0.070 - 0.105: 173 0.105 - 0.140: 143 0.140 - 0.174: 18 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CB THR M 116 " pdb=" CA THR M 116 " pdb=" OG1 THR M 116 " pdb=" CG2 THR M 116 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CB THR P 116 " pdb=" CA THR P 116 " pdb=" OG1 THR P 116 " pdb=" CG2 THR P 116 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CB THR C 116 " pdb=" CA THR C 116 " pdb=" OG1 THR C 116 " pdb=" CG2 THR C 116 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1833 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 129 " 0.157 9.50e-02 1.11e+02 7.06e-02 3.64e+00 pdb=" NE ARG J 129 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG J 129 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG J 129 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG J 129 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 129 " 0.157 9.50e-02 1.11e+02 7.06e-02 3.64e+00 pdb=" NE ARG C 129 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 129 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 129 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 129 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 129 " 0.156 9.50e-02 1.11e+02 7.05e-02 3.63e+00 pdb=" NE ARG G 129 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG G 129 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 129 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 129 " 0.001 2.00e-02 2.50e+03 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2702 2.78 - 3.31: 10153 3.31 - 3.84: 18013 3.84 - 4.37: 21631 4.37 - 4.90: 38953 Nonbonded interactions: 91452 Sorted by model distance: nonbonded pdb=" O GLU M 96 " pdb=" ND2 ASN M 101 " model vdw 2.251 3.120 nonbonded pdb=" O GLU H 96 " pdb=" ND2 ASN H 101 " model vdw 2.251 3.120 nonbonded pdb=" O GLU L 96 " pdb=" ND2 ASN L 101 " model vdw 2.251 3.120 nonbonded pdb=" O GLU N 96 " pdb=" ND2 ASN N 101 " model vdw 2.252 3.120 nonbonded pdb=" O GLU P 96 " pdb=" ND2 ASN P 101 " model vdw 2.252 3.120 ... (remaining 91447 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.400 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.006 0.050 12006 Z= 0.266 Angle : 0.774 4.817 16236 Z= 0.415 Chirality : 0.054 0.174 1836 Planarity : 0.008 0.071 2016 Dihedral : 15.351 71.680 4482 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 23.94 % Favored : 76.06 % 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 aren not related in a simple way. whole: -4.04 (0.20), residues: 1386 helix: -1.47 (0.34), residues: 144 sheet: -2.64 (0.22), residues: 450 loop : -3.02 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG J 129 TYR 0.013 0.002 TYR D 160 PHE 0.028 0.004 PHE R 117 TRP 0.011 0.002 TRP B 123 HIS 0.003 0.002 HIS F 139 Details of bonding type rmsd covalent geometry : bond 0.00587 (12006) covalent geometry : angle 0.77389 (16236) hydrogen bonds : bond 0.22412 ( 360) hydrogen bonds : angle 10.82741 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8194 (mmtp) REVERT: A 115 MET cc_start: 0.8685 (mtp) cc_final: 0.8463 (ttm) REVERT: A 124 ASN cc_start: 0.9260 (t0) cc_final: 0.9042 (t0) REVERT: B 109 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8130 (mmtp) REVERT: B 115 MET cc_start: 0.8857 (mtp) cc_final: 0.8565 (ttm) REVERT: B 164 ASP cc_start: 0.8260 (t0) cc_final: 0.8026 (t0) REVERT: C 109 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8251 (mmtp) REVERT: C 126 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7945 (mmmm) REVERT: C 164 ASP cc_start: 0.8290 (t0) cc_final: 0.7982 (t0) REVERT: D 109 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8189 (mmtp) REVERT: D 164 ASP cc_start: 0.8381 (t0) cc_final: 0.8132 (t0) REVERT: E 109 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8191 (mmtp) REVERT: E 164 ASP cc_start: 0.8382 (t0) cc_final: 0.8167 (t0) REVERT: F 109 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp) REVERT: G 109 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8198 (mmtm) REVERT: H 109 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8164 (mmtp) REVERT: I 107 ARG cc_start: 0.8711 (mtp-110) cc_final: 0.8479 (mtp85) REVERT: J 126 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8215 (mmmt) REVERT: L 164 ASP cc_start: 0.8235 (t0) cc_final: 0.8022 (t0) REVERT: O 126 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8253 (mmmm) REVERT: O 151 TYR cc_start: 0.8662 (m-80) cc_final: 0.8388 (m-80) REVERT: P 107 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8429 (mtm110) REVERT: P 114 TYR cc_start: 0.8984 (m-80) cc_final: 0.8736 (m-80) REVERT: Q 119 ASN cc_start: 0.7979 (m110) cc_final: 0.7658 (m-40) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.1897 time to fit residues: 97.2012 Evaluate side-chains 378 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN F 124 ASN J 124 ASN K 106 ASN L 106 ASN M 106 ASN O 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113770 restraints weight = 13949.066| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.07 r_work: 0.3188 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12006 Z= 0.128 Angle : 0.576 4.708 16236 Z= 0.316 Chirality : 0.050 0.147 1836 Planarity : 0.005 0.032 2016 Dihedral : 4.532 19.958 1602 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.78 % Allowed : 23.40 % Favored : 75.82 % 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 aren not related in a simple way. whole: -3.81 (0.21), residues: 1386 helix: -0.91 (0.41), residues: 180 sheet: -2.95 (0.18), residues: 702 loop : -2.08 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 104 TYR 0.014 0.001 TYR K 160 PHE 0.020 0.002 PHE M 117 TRP 0.014 0.002 TRP M 123 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00288 (12006) covalent geometry : angle 0.57579 (16236) hydrogen bonds : bond 0.05320 ( 360) hydrogen bonds : angle 7.61673 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 361 time to evaluate : 0.473 Fit side-chains REVERT: B 109 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8329 (mmtp) REVERT: C 109 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8483 (mmtp) REVERT: D 109 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8417 (mmtp) REVERT: D 119 ASN cc_start: 0.8479 (m110) cc_final: 0.8258 (m-40) REVERT: E 109 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8423 (mmtp) REVERT: E 119 ASN cc_start: 0.8440 (m110) cc_final: 0.8168 (m-40) REVERT: F 137 ARG cc_start: 0.8703 (ptp-170) cc_final: 0.8483 (ptp-170) REVERT: F 153 LEU cc_start: 0.9171 (mt) cc_final: 0.8952 (mt) REVERT: G 95 GLU cc_start: 0.8720 (mp0) cc_final: 0.8495 (mp0) REVERT: G 109 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8478 (mmtm) REVERT: G 119 ASN cc_start: 0.8439 (m110) cc_final: 0.8236 (m110) REVERT: H 109 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8417 (mmtp) REVERT: H 119 ASN cc_start: 0.8402 (m110) cc_final: 0.8179 (m110) REVERT: K 119 ASN cc_start: 0.8540 (m110) cc_final: 0.8268 (m110) REVERT: L 107 ARG cc_start: 0.8786 (mtp-110) cc_final: 0.8535 (mtp85) REVERT: N 119 ASN cc_start: 0.8615 (m110) cc_final: 0.8396 (m-40) REVERT: O 119 ASN cc_start: 0.8557 (m110) cc_final: 0.8356 (m110) REVERT: O 151 TYR cc_start: 0.9067 (m-80) cc_final: 0.8768 (m-80) REVERT: Q 119 ASN cc_start: 0.8547 (m110) cc_final: 0.8336 (m-40) REVERT: R 119 ASN cc_start: 0.8616 (m110) cc_final: 0.8360 (m110) outliers start: 10 outliers final: 4 residues processed: 364 average time/residue: 0.1735 time to fit residues: 80.6153 Evaluate side-chains 353 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 349 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain Q residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 65 optimal weight: 0.3980 chunk 7 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 ASN N 124 ASN Q 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105249 restraints weight = 14877.923| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.40 r_work: 0.3058 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.005 0.037 12006 Z= 0.201 Angle : 0.595 4.911 16236 Z= 0.329 Chirality : 0.053 0.179 1836 Planarity : 0.004 0.037 2016 Dihedral : 4.451 22.088 1602 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.23 % Allowed : 24.02 % Favored : 71.75 % 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 aren not related in a simple way. whole: -3.29 (0.22), residues: 1386 helix: -0.86 (0.40), residues: 180 sheet: -2.51 (0.19), residues: 594 loop : -2.05 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 129 TYR 0.013 0.002 TYR C 160 PHE 0.024 0.003 PHE M 117 TRP 0.011 0.002 TRP R 123 HIS 0.004 0.002 HIS I 139 Details of bonding type rmsd covalent geometry : bond 0.00458 (12006) covalent geometry : angle 0.59465 (16236) hydrogen bonds : bond 0.05690 ( 360) hydrogen bonds : angle 7.27488 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 366 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: B 109 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8195 (mmtp) REVERT: B 164 ASP cc_start: 0.8735 (t0) cc_final: 0.8446 (t0) REVERT: C 109 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8242 (mmtp) REVERT: D 119 ASN cc_start: 0.8519 (m110) cc_final: 0.8211 (m110) REVERT: E 109 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8192 (mmtp) REVERT: E 164 ASP cc_start: 0.8825 (t70) cc_final: 0.8343 (t0) REVERT: G 119 ASN cc_start: 0.8440 (m110) cc_final: 0.8108 (m110) REVERT: H 109 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8197 (mmtp) REVERT: H 119 ASN cc_start: 0.8471 (m110) cc_final: 0.8149 (m110) REVERT: H 159 ASP cc_start: 0.8743 (m-30) cc_final: 0.8542 (m-30) REVERT: I 92 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8135 (mt) REVERT: K 104 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7164 (mtp180) REVERT: K 119 ASN cc_start: 0.8558 (m110) cc_final: 0.8132 (m110) REVERT: K 164 ASP cc_start: 0.8751 (t70) cc_final: 0.8529 (t0) REVERT: L 107 ARG cc_start: 0.8747 (mtp-110) cc_final: 0.8525 (mtp85) REVERT: N 119 ASN cc_start: 0.8632 (m110) cc_final: 0.8264 (m-40) REVERT: N 159 ASP cc_start: 0.8703 (m-30) cc_final: 0.8483 (m-30) REVERT: O 119 ASN cc_start: 0.8611 (m110) cc_final: 0.8270 (m110) REVERT: P 92 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8060 (mp) REVERT: Q 119 ASN cc_start: 0.8680 (m110) cc_final: 0.8381 (m110) REVERT: R 119 ASN cc_start: 0.8687 (m110) cc_final: 0.8277 (m110) outliers start: 54 outliers final: 20 residues processed: 413 average time/residue: 0.1625 time to fit residues: 86.8943 Evaluate side-chains 383 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 361 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 106 ASN J 124 ASN Q 106 ASN Q 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102876 restraints weight = 15084.560| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.40 r_work: 0.3033 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12006 Z= 0.246 Angle : 0.627 5.001 16236 Z= 0.345 Chirality : 0.054 0.195 1836 Planarity : 0.005 0.042 2016 Dihedral : 4.498 21.685 1602 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.76 % Allowed : 25.90 % Favored : 70.34 % 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 aren not related in a simple way. whole: -3.08 (0.22), residues: 1386 helix: -0.85 (0.39), residues: 180 sheet: -2.20 (0.20), residues: 594 loop : -2.07 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 129 TYR 0.014 0.002 TYR J 151 PHE 0.021 0.002 PHE B 117 TRP 0.012 0.002 TRP I 123 HIS 0.005 0.002 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00565 (12006) covalent geometry : angle 0.62715 (16236) hydrogen bonds : bond 0.05742 ( 360) hydrogen bonds : angle 7.13903 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 364 time to evaluate : 0.479 Fit side-chains REVERT: B 164 ASP cc_start: 0.8826 (t0) cc_final: 0.8482 (t0) REVERT: C 109 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8286 (mmtp) REVERT: C 122 GLU cc_start: 0.8494 (mp0) cc_final: 0.7935 (mp0) REVERT: D 119 ASN cc_start: 0.8551 (m110) cc_final: 0.8221 (m110) REVERT: D 164 ASP cc_start: 0.8870 (t0) cc_final: 0.8504 (t0) REVERT: E 122 GLU cc_start: 0.8303 (mp0) cc_final: 0.7782 (mp0) REVERT: E 164 ASP cc_start: 0.8819 (t70) cc_final: 0.8146 (t0) REVERT: G 119 ASN cc_start: 0.8484 (m110) cc_final: 0.8253 (m110) REVERT: G 121 LYS cc_start: 0.8588 (tptp) cc_final: 0.8327 (ttpt) REVERT: G 122 GLU cc_start: 0.8382 (mp0) cc_final: 0.7279 (mp0) REVERT: H 109 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8207 (mmtp) REVERT: H 119 ASN cc_start: 0.8597 (m110) cc_final: 0.8331 (m110) REVERT: H 122 GLU cc_start: 0.8442 (mp0) cc_final: 0.7849 (mp0) REVERT: H 164 ASP cc_start: 0.8872 (t0) cc_final: 0.8590 (t0) REVERT: I 92 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8207 (mt) REVERT: I 121 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7813 (ttpp) REVERT: J 122 GLU cc_start: 0.8556 (mp0) cc_final: 0.8070 (mp0) REVERT: K 119 ASN cc_start: 0.8603 (m110) cc_final: 0.8353 (m110) REVERT: K 164 ASP cc_start: 0.8694 (t70) cc_final: 0.8460 (t0) REVERT: L 92 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8243 (mp) REVERT: L 121 LYS cc_start: 0.8438 (ttpt) cc_final: 0.7958 (ttpp) REVERT: M 137 ARG cc_start: 0.8871 (ptp-170) cc_final: 0.8541 (ptp-170) REVERT: N 119 ASN cc_start: 0.8653 (m110) cc_final: 0.8315 (m-40) REVERT: O 119 ASN cc_start: 0.8624 (m110) cc_final: 0.8321 (m110) REVERT: P 92 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8064 (mp) REVERT: P 164 ASP cc_start: 0.8941 (t0) cc_final: 0.8654 (t0) REVERT: Q 119 ASN cc_start: 0.8615 (m110) cc_final: 0.8315 (m110) REVERT: Q 121 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7968 (ttpt) REVERT: R 110 THR cc_start: 0.8922 (m) cc_final: 0.8559 (p) REVERT: R 119 ASN cc_start: 0.8697 (m110) cc_final: 0.8283 (m110) REVERT: R 164 ASP cc_start: 0.8683 (t0) cc_final: 0.8353 (t0) outliers start: 48 outliers final: 30 residues processed: 403 average time/residue: 0.1600 time to fit residues: 83.9629 Evaluate side-chains 395 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 362 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 106 ASN C 106 ASN C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN E 106 ASN J 124 ASN O 106 ASN O 124 ASN Q 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104968 restraints weight = 14913.396| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.38 r_work: 0.3048 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12006 Z= 0.178 Angle : 0.586 5.441 16236 Z= 0.322 Chirality : 0.052 0.192 1836 Planarity : 0.004 0.043 2016 Dihedral : 4.393 20.836 1602 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.46 % Allowed : 26.84 % Favored : 68.70 % 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 aren not related in a simple way. whole: -2.95 (0.22), residues: 1386 helix: -0.61 (0.40), residues: 180 sheet: -2.17 (0.20), residues: 594 loop : -1.98 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 129 TYR 0.013 0.001 TYR J 151 PHE 0.016 0.002 PHE M 117 TRP 0.011 0.002 TRP Q 123 HIS 0.003 0.002 HIS R 139 Details of bonding type rmsd covalent geometry : bond 0.00405 (12006) covalent geometry : angle 0.58626 (16236) hydrogen bonds : bond 0.05368 ( 360) hydrogen bonds : angle 6.80542 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 356 time to evaluate : 0.449 Fit side-chains REVERT: B 109 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8211 (mmtp) REVERT: B 164 ASP cc_start: 0.8733 (t0) cc_final: 0.8380 (t0) REVERT: C 109 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8291 (mmtp) REVERT: C 122 GLU cc_start: 0.8471 (mp0) cc_final: 0.7981 (mp0) REVERT: D 119 ASN cc_start: 0.8538 (m110) cc_final: 0.8208 (m110) REVERT: D 164 ASP cc_start: 0.8839 (t0) cc_final: 0.8465 (t0) REVERT: E 122 GLU cc_start: 0.8284 (mp0) cc_final: 0.7744 (mp0) REVERT: E 164 ASP cc_start: 0.8807 (t70) cc_final: 0.8104 (t0) REVERT: G 119 ASN cc_start: 0.8471 (m110) cc_final: 0.8224 (m110) REVERT: G 121 LYS cc_start: 0.8605 (tptp) cc_final: 0.8331 (ttpt) REVERT: G 122 GLU cc_start: 0.8379 (mp0) cc_final: 0.7407 (mp0) REVERT: H 109 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8210 (mmtp) REVERT: H 119 ASN cc_start: 0.8588 (m110) cc_final: 0.8302 (m110) REVERT: H 122 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: H 153 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9015 (mt) REVERT: I 92 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8094 (mp) REVERT: I 121 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7879 (ttpt) REVERT: J 122 GLU cc_start: 0.8529 (mp0) cc_final: 0.8049 (mp0) REVERT: K 119 ASN cc_start: 0.8545 (m110) cc_final: 0.8273 (m110) REVERT: K 164 ASP cc_start: 0.8689 (t70) cc_final: 0.8470 (t0) REVERT: L 121 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8174 (ttpt) REVERT: N 119 ASN cc_start: 0.8615 (m110) cc_final: 0.8316 (m110) REVERT: O 119 ASN cc_start: 0.8598 (m110) cc_final: 0.8268 (m110) REVERT: O 151 TYR cc_start: 0.9054 (m-80) cc_final: 0.8814 (m-80) REVERT: Q 119 ASN cc_start: 0.8647 (m110) cc_final: 0.8329 (m110) REVERT: Q 121 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8047 (ttpt) REVERT: R 119 ASN cc_start: 0.8626 (m110) cc_final: 0.8335 (m110) outliers start: 57 outliers final: 32 residues processed: 404 average time/residue: 0.1574 time to fit residues: 83.1643 Evaluate side-chains 391 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 ASN O 124 ASN Q 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103351 restraints weight = 14976.353| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.41 r_work: 0.3048 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12006 Z= 0.220 Angle : 0.615 5.679 16236 Z= 0.337 Chirality : 0.053 0.219 1836 Planarity : 0.005 0.048 2016 Dihedral : 4.432 20.900 1602 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.01 % Allowed : 26.53 % Favored : 68.47 % 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 aren not related in a simple way. whole: -2.83 (0.22), residues: 1386 helix: -0.58 (0.39), residues: 180 sheet: -2.06 (0.20), residues: 594 loop : -1.91 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 129 TYR 0.013 0.001 TYR J 151 PHE 0.017 0.002 PHE P 117 TRP 0.011 0.002 TRP K 123 HIS 0.004 0.002 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00506 (12006) covalent geometry : angle 0.61471 (16236) hydrogen bonds : bond 0.05613 ( 360) hydrogen bonds : angle 6.85295 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 370 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8545 (tptp) cc_final: 0.8319 (ttpp) REVERT: A 164 ASP cc_start: 0.9052 (t0) cc_final: 0.8502 (t0) REVERT: B 109 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8219 (mmtp) REVERT: B 122 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: B 164 ASP cc_start: 0.8804 (t0) cc_final: 0.8453 (t0) REVERT: C 109 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8306 (mmtp) REVERT: C 122 GLU cc_start: 0.8482 (mp0) cc_final: 0.8001 (mp0) REVERT: D 119 ASN cc_start: 0.8577 (m110) cc_final: 0.8261 (m110) REVERT: D 122 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: E 122 GLU cc_start: 0.8290 (mp0) cc_final: 0.7747 (mp0) REVERT: E 164 ASP cc_start: 0.8810 (t70) cc_final: 0.8121 (t0) REVERT: F 122 GLU cc_start: 0.8311 (mp0) cc_final: 0.7901 (mp0) REVERT: F 153 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8877 (mt) REVERT: G 119 ASN cc_start: 0.8523 (m110) cc_final: 0.8247 (m110) REVERT: G 121 LYS cc_start: 0.8632 (tptp) cc_final: 0.8357 (ttpt) REVERT: G 122 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: H 109 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8194 (mmtp) REVERT: H 119 ASN cc_start: 0.8590 (m110) cc_final: 0.8283 (m110) REVERT: H 122 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: H 164 ASP cc_start: 0.8839 (t0) cc_final: 0.8533 (t0) REVERT: I 92 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8136 (mp) REVERT: I 110 THR cc_start: 0.8992 (m) cc_final: 0.8555 (p) REVERT: I 121 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7894 (ttpt) REVERT: J 122 GLU cc_start: 0.8513 (mp0) cc_final: 0.8168 (mp0) REVERT: J 153 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9040 (mt) REVERT: K 119 ASN cc_start: 0.8536 (m110) cc_final: 0.8252 (m110) REVERT: K 164 ASP cc_start: 0.8714 (t70) cc_final: 0.8477 (t0) REVERT: L 110 THR cc_start: 0.8942 (m) cc_final: 0.8598 (p) REVERT: L 121 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7864 (ttpp) REVERT: N 119 ASN cc_start: 0.8611 (m110) cc_final: 0.8215 (m-40) REVERT: O 119 ASN cc_start: 0.8587 (m110) cc_final: 0.8237 (m110) REVERT: P 164 ASP cc_start: 0.8936 (t0) cc_final: 0.8640 (t0) REVERT: Q 119 ASN cc_start: 0.8616 (m110) cc_final: 0.8288 (m110) REVERT: Q 121 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8111 (ttpt) REVERT: R 110 THR cc_start: 0.8937 (m) cc_final: 0.8575 (p) REVERT: R 119 ASN cc_start: 0.8620 (m110) cc_final: 0.8316 (m110) REVERT: R 164 ASP cc_start: 0.8645 (t0) cc_final: 0.8391 (t0) outliers start: 64 outliers final: 37 residues processed: 423 average time/residue: 0.1611 time to fit residues: 89.0405 Evaluate side-chains 410 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 366 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 137 ARG Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN J 124 ASN N 124 ASN O 124 ASN Q 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103939 restraints weight = 15015.613| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.42 r_work: 0.3054 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12006 Z= 0.205 Angle : 0.616 5.496 16236 Z= 0.337 Chirality : 0.054 0.223 1836 Planarity : 0.005 0.053 2016 Dihedral : 4.420 20.444 1602 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.16 % Allowed : 26.60 % Favored : 68.23 % 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 aren not related in a simple way. whole: -2.76 (0.22), residues: 1386 helix: -0.60 (0.38), residues: 180 sheet: -2.01 (0.20), residues: 594 loop : -1.86 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 129 TYR 0.014 0.001 TYR J 151 PHE 0.017 0.002 PHE P 117 TRP 0.010 0.002 TRP N 123 HIS 0.003 0.002 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00474 (12006) covalent geometry : angle 0.61574 (16236) hydrogen bonds : bond 0.05518 ( 360) hydrogen bonds : angle 6.72078 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 361 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8547 (tptp) cc_final: 0.8298 (ttpp) REVERT: A 129 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7948 (ttm110) REVERT: B 109 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8189 (mmtp) REVERT: B 122 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 164 ASP cc_start: 0.8825 (t0) cc_final: 0.8487 (t0) REVERT: C 109 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8289 (mmtp) REVERT: C 122 GLU cc_start: 0.8513 (mp0) cc_final: 0.8003 (mp0) REVERT: D 119 ASN cc_start: 0.8582 (m110) cc_final: 0.8247 (m110) REVERT: D 122 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: E 103 LEU cc_start: 0.8531 (mt) cc_final: 0.8272 (mt) REVERT: E 109 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8231 (mmtp) REVERT: E 115 MET cc_start: 0.9316 (mtp) cc_final: 0.9099 (mtm) REVERT: E 122 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: E 164 ASP cc_start: 0.8866 (t70) cc_final: 0.8187 (t0) REVERT: F 153 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8901 (mt) REVERT: G 119 ASN cc_start: 0.8521 (m110) cc_final: 0.8229 (m110) REVERT: G 121 LYS cc_start: 0.8633 (tptp) cc_final: 0.8351 (ttpt) REVERT: G 122 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: H 109 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8157 (mmtp) REVERT: H 119 ASN cc_start: 0.8562 (m110) cc_final: 0.8269 (m110) REVERT: H 122 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: H 164 ASP cc_start: 0.8837 (t0) cc_final: 0.8529 (t0) REVERT: I 92 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8115 (mp) REVERT: I 121 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7881 (ttpt) REVERT: J 122 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: J 153 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8961 (mt) REVERT: K 164 ASP cc_start: 0.8712 (t70) cc_final: 0.8492 (t0) REVERT: L 110 THR cc_start: 0.8944 (m) cc_final: 0.8595 (p) REVERT: L 121 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8187 (ttpt) REVERT: M 110 THR cc_start: 0.8971 (m) cc_final: 0.8644 (p) REVERT: N 119 ASN cc_start: 0.8541 (m110) cc_final: 0.8253 (m110) REVERT: O 119 ASN cc_start: 0.8613 (m110) cc_final: 0.8252 (m110) REVERT: P 164 ASP cc_start: 0.8939 (t0) cc_final: 0.8652 (t0) REVERT: Q 119 ASN cc_start: 0.8669 (m110) cc_final: 0.8323 (m110) REVERT: Q 121 LYS cc_start: 0.8421 (ttpt) cc_final: 0.8094 (ttpt) REVERT: R 110 THR cc_start: 0.8944 (m) cc_final: 0.8588 (p) REVERT: R 119 ASN cc_start: 0.8641 (m110) cc_final: 0.8319 (m110) REVERT: R 164 ASP cc_start: 0.8651 (t0) cc_final: 0.8341 (t0) outliers start: 66 outliers final: 40 residues processed: 412 average time/residue: 0.1618 time to fit residues: 86.6684 Evaluate side-chains 405 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 137 ARG Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN C 124 ASN G 106 ASN J 124 ASN O 124 ASN P 124 ASN Q 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104008 restraints weight = 14903.621| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.42 r_work: 0.3058 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12006 Z= 0.201 Angle : 0.622 5.874 16236 Z= 0.338 Chirality : 0.053 0.218 1836 Planarity : 0.005 0.057 2016 Dihedral : 4.430 20.012 1602 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.63 % Allowed : 25.74 % Favored : 68.62 % 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 aren not related in a simple way. whole: -2.71 (0.22), residues: 1386 helix: -0.58 (0.39), residues: 180 sheet: -1.96 (0.20), residues: 594 loop : -1.83 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG H 129 TYR 0.014 0.001 TYR J 151 PHE 0.016 0.002 PHE P 117 TRP 0.011 0.002 TRP M 123 HIS 0.003 0.002 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00466 (12006) covalent geometry : angle 0.62176 (16236) hydrogen bonds : bond 0.05508 ( 360) hydrogen bonds : angle 6.67479 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 355 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8525 (tptp) cc_final: 0.8276 (ttpp) REVERT: A 129 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7956 (ttm110) REVERT: B 109 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8234 (mmtp) REVERT: B 122 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: B 153 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8979 (mt) REVERT: B 164 ASP cc_start: 0.8812 (t0) cc_final: 0.8229 (t0) REVERT: C 109 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8323 (mmtp) REVERT: C 122 GLU cc_start: 0.8484 (mp0) cc_final: 0.7978 (mp0) REVERT: D 95 GLU cc_start: 0.8849 (mp0) cc_final: 0.8077 (mp0) REVERT: D 119 ASN cc_start: 0.8558 (m110) cc_final: 0.8219 (m110) REVERT: D 122 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: E 103 LEU cc_start: 0.8540 (mt) cc_final: 0.8274 (mt) REVERT: E 109 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8182 (mmtp) REVERT: E 115 MET cc_start: 0.9294 (mtp) cc_final: 0.9077 (mtm) REVERT: E 122 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: E 153 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8946 (mt) REVERT: E 164 ASP cc_start: 0.8796 (t70) cc_final: 0.8124 (t0) REVERT: F 153 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8823 (mt) REVERT: G 95 GLU cc_start: 0.8992 (mp0) cc_final: 0.8566 (mp0) REVERT: G 119 ASN cc_start: 0.8515 (m110) cc_final: 0.8269 (m110) REVERT: G 121 LYS cc_start: 0.8553 (tptp) cc_final: 0.8316 (ttpt) REVERT: G 122 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: H 109 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8220 (mmtp) REVERT: H 119 ASN cc_start: 0.8501 (m110) cc_final: 0.8205 (m110) REVERT: H 122 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: H 164 ASP cc_start: 0.8804 (t0) cc_final: 0.8497 (t0) REVERT: I 110 THR cc_start: 0.8952 (m) cc_final: 0.8514 (p) REVERT: I 121 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7837 (ttpt) REVERT: J 122 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: J 153 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9020 (mt) REVERT: K 164 ASP cc_start: 0.8681 (t70) cc_final: 0.8459 (t0) REVERT: L 110 THR cc_start: 0.8931 (m) cc_final: 0.8556 (p) REVERT: L 121 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8136 (ttpt) REVERT: M 110 THR cc_start: 0.8963 (m) cc_final: 0.8644 (p) REVERT: O 119 ASN cc_start: 0.8603 (m110) cc_final: 0.8265 (m110) REVERT: P 164 ASP cc_start: 0.8898 (t0) cc_final: 0.8609 (t0) REVERT: Q 121 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8088 (ttpt) REVERT: R 110 THR cc_start: 0.8940 (m) cc_final: 0.8585 (p) REVERT: R 119 ASN cc_start: 0.8612 (m110) cc_final: 0.8327 (m110) REVERT: R 164 ASP cc_start: 0.8670 (t0) cc_final: 0.8374 (t0) outliers start: 72 outliers final: 43 residues processed: 411 average time/residue: 0.1676 time to fit residues: 88.8768 Evaluate side-chains 403 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 350 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.0000 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN G 106 ASN J 124 ASN N 124 ASN O 124 ASN Q 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109651 restraints weight = 14641.694| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.36 r_work: 0.3130 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12006 Z= 0.118 Angle : 0.585 5.714 16236 Z= 0.318 Chirality : 0.051 0.182 1836 Planarity : 0.005 0.059 2016 Dihedral : 4.260 17.797 1602 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.30 % Allowed : 27.46 % Favored : 68.23 % 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 aren not related in a simple way. whole: -2.44 (0.22), residues: 1386 helix: -0.46 (0.39), residues: 180 sheet: -1.67 (0.20), residues: 504 loop : -1.84 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG D 129 TYR 0.012 0.001 TYR N 114 PHE 0.012 0.001 PHE P 117 TRP 0.010 0.002 TRP M 123 HIS 0.004 0.001 HIS Q 139 Details of bonding type rmsd covalent geometry : bond 0.00267 (12006) covalent geometry : angle 0.58521 (16236) hydrogen bonds : bond 0.05054 ( 360) hydrogen bonds : angle 6.35942 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 343 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: B 95 GLU cc_start: 0.8757 (mp0) cc_final: 0.7982 (mp0) REVERT: B 109 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8223 (mmtp) REVERT: B 122 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 153 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9039 (mt) REVERT: C 109 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8327 (mmtp) REVERT: C 122 GLU cc_start: 0.8465 (mp0) cc_final: 0.8008 (mp0) REVERT: D 95 GLU cc_start: 0.8758 (mp0) cc_final: 0.7975 (mp0) REVERT: D 119 ASN cc_start: 0.8478 (m110) cc_final: 0.8235 (m110) REVERT: D 122 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: E 109 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8227 (mmtp) REVERT: E 122 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: E 153 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8974 (mt) REVERT: F 95 GLU cc_start: 0.8790 (mp0) cc_final: 0.8541 (mp0) REVERT: F 122 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: F 153 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8929 (mt) REVERT: G 95 GLU cc_start: 0.8952 (mp0) cc_final: 0.8559 (mp0) REVERT: G 119 ASN cc_start: 0.8406 (m110) cc_final: 0.8167 (m110) REVERT: G 122 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: H 109 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8264 (mmtp) REVERT: H 119 ASN cc_start: 0.8434 (m110) cc_final: 0.8184 (m110) REVERT: H 122 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: I 121 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7751 (ttpp) REVERT: J 122 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: L 110 THR cc_start: 0.8874 (m) cc_final: 0.8472 (p) REVERT: L 121 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8088 (ttpt) REVERT: M 151 TYR cc_start: 0.8950 (m-80) cc_final: 0.8715 (m-80) REVERT: Q 121 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8011 (ttpt) REVERT: R 119 ASN cc_start: 0.8444 (m110) cc_final: 0.8229 (m110) outliers start: 55 outliers final: 29 residues processed: 387 average time/residue: 0.1578 time to fit residues: 79.5833 Evaluate side-chains 382 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 342 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN B 124 ASN D 124 ASN J 124 ASN N 124 ASN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101147 restraints weight = 15080.918| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.43 r_work: 0.2998 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 12006 Z= 0.332 Angle : 0.721 6.191 16236 Z= 0.390 Chirality : 0.058 0.247 1836 Planarity : 0.006 0.063 2016 Dihedral : 4.651 20.333 1602 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.29 % Allowed : 28.01 % Favored : 68.70 % 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 aren not related in a simple way. whole: -2.41 (0.22), residues: 1386 helix: -0.75 (0.37), residues: 180 sheet: -1.55 (0.22), residues: 522 loop : -1.80 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG H 129 TYR 0.018 0.002 TYR J 151 PHE 0.018 0.002 PHE H 117 TRP 0.025 0.003 TRP E 123 HIS 0.005 0.002 HIS G 139 Details of bonding type rmsd covalent geometry : bond 0.00778 (12006) covalent geometry : angle 0.72096 (16236) hydrogen bonds : bond 0.06161 ( 360) hydrogen bonds : angle 6.84660 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.487 Fit side-chains REVERT: A 122 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: A 164 ASP cc_start: 0.9020 (t0) cc_final: 0.8365 (t0) REVERT: B 109 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8128 (mmtp) REVERT: B 110 THR cc_start: 0.8979 (m) cc_final: 0.8655 (p) REVERT: B 122 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: B 164 ASP cc_start: 0.8809 (t0) cc_final: 0.8369 (t0) REVERT: C 109 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8289 (mmtp) REVERT: C 122 GLU cc_start: 0.8515 (mp0) cc_final: 0.7965 (mp0) REVERT: D 95 GLU cc_start: 0.8921 (mp0) cc_final: 0.8099 (mp0) REVERT: D 119 ASN cc_start: 0.8600 (m110) cc_final: 0.8163 (m110) REVERT: D 122 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: D 164 ASP cc_start: 0.8643 (t0) cc_final: 0.8218 (t0) REVERT: E 109 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8173 (mmtp) REVERT: E 164 ASP cc_start: 0.8865 (t70) cc_final: 0.8255 (t0) REVERT: F 121 LYS cc_start: 0.8546 (tptp) cc_final: 0.8096 (ttpt) REVERT: F 122 GLU cc_start: 0.8393 (mp0) cc_final: 0.7570 (mp0) REVERT: G 95 GLU cc_start: 0.9043 (mp0) cc_final: 0.8727 (mp0) REVERT: G 119 ASN cc_start: 0.8548 (m110) cc_final: 0.8229 (m110) REVERT: G 122 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: H 109 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8161 (mmtp) REVERT: H 119 ASN cc_start: 0.8526 (m110) cc_final: 0.8195 (m110) REVERT: H 122 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: I 110 THR cc_start: 0.8954 (m) cc_final: 0.8557 (p) REVERT: I 121 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7862 (ttpt) REVERT: J 122 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: K 110 THR cc_start: 0.8987 (m) cc_final: 0.8697 (p) REVERT: L 110 THR cc_start: 0.8957 (m) cc_final: 0.8615 (p) REVERT: L 121 LYS cc_start: 0.8430 (ttpt) cc_final: 0.7734 (ttpt) REVERT: L 122 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: L 164 ASP cc_start: 0.8753 (t0) cc_final: 0.8377 (t0) REVERT: N 110 THR cc_start: 0.8970 (m) cc_final: 0.8520 (p) REVERT: O 110 THR cc_start: 0.8961 (m) cc_final: 0.8641 (p) REVERT: P 110 THR cc_start: 0.8818 (m) cc_final: 0.8459 (p) REVERT: P 122 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: P 164 ASP cc_start: 0.8997 (t0) cc_final: 0.8719 (t0) REVERT: Q 121 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8121 (ttpt) REVERT: R 110 THR cc_start: 0.8920 (m) cc_final: 0.8595 (p) REVERT: R 119 ASN cc_start: 0.8661 (m110) cc_final: 0.8347 (m110) REVERT: R 164 ASP cc_start: 0.8647 (t0) cc_final: 0.8427 (t0) outliers start: 42 outliers final: 22 residues processed: 397 average time/residue: 0.1751 time to fit residues: 88.8616 Evaluate side-chains 392 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 362 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 122 GLU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 0.0020 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN C 124 ASN J 124 ASN L 106 ASN N 124 ASN Q 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108543 restraints weight = 14502.311| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.39 r_work: 0.3119 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12006 Z= 0.123 Angle : 0.612 5.750 16236 Z= 0.331 Chirality : 0.051 0.188 1836 Planarity : 0.006 0.064 2016 Dihedral : 4.420 18.070 1602 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.13 % Allowed : 28.17 % Favored : 68.70 % 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 aren not related in a simple way. whole: -2.13 (0.22), residues: 1386 helix: -0.58 (0.39), residues: 180 sheet: -1.13 (0.23), residues: 432 loop : -1.80 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 129 TYR 0.012 0.001 TYR J 151 PHE 0.012 0.001 PHE O 117 TRP 0.016 0.002 TRP E 123 HIS 0.005 0.001 HIS Q 139 Details of bonding type rmsd covalent geometry : bond 0.00282 (12006) covalent geometry : angle 0.61166 (16236) hydrogen bonds : bond 0.05185 ( 360) hydrogen bonds : angle 6.40970 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.20 seconds wall clock time: 53 minutes 27.10 seconds (3207.10 seconds total)