Starting phenix.real_space_refine on Sat Jan 18 03:36:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zra_60394/01_2025/8zra_60394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zra_60394/01_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_60394/01_2025/8zra_60394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zra_60394/01_2025/8zra_60394.map" model { file = "/net/cci-nas-00/data/ceres_data/8zra_60394/01_2025/8zra_60394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zra_60394/01_2025/8zra_60394.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 3.05, per 1000 atoms: 0.26 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: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.44 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: 2.81 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' 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: 1.090 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 22.480 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- 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= 0.382 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP B 123 HIS 0.003 0.002 HIS F 139 PHE 0.028 0.004 PHE R 117 TYR 0.013 0.002 TYR D 160 ARG 0.013 0.002 ARG J 129 *********************** 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 : 1.239 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: 0.3931 time to fit residues: 201.2506 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 : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN J 124 ASN K 106 ASN L 106 ASN M 106 ASN O 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107544 restraints weight = 14058.547| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.04 r_work: 0.3087 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12006 Z= 0.331 Angle : 0.636 4.785 16236 Z= 0.349 Chirality : 0.053 0.172 1836 Planarity : 0.005 0.033 2016 Dihedral : 4.696 21.595 1602 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.68 % Allowed : 22.46 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.20), residues: 1386 helix: -1.01 (0.40), residues: 180 sheet: -2.90 (0.18), residues: 684 loop : -2.87 (0.21), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 123 HIS 0.005 0.002 HIS I 139 PHE 0.026 0.003 PHE M 117 TYR 0.015 0.002 TYR K 160 ARG 0.009 0.001 ARG H 104 *********************** 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 421 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 374 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: B 109 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8356 (mmtp) REVERT: B 119 ASN cc_start: 0.8502 (m110) cc_final: 0.8249 (m-40) REVERT: C 109 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8498 (mmtp) REVERT: D 164 ASP cc_start: 0.8667 (t0) cc_final: 0.8462 (t0) REVERT: E 119 ASN cc_start: 0.8427 (m110) cc_final: 0.8154 (m-40) REVERT: E 164 ASP cc_start: 0.8767 (t0) cc_final: 0.8336 (t0) REVERT: F 137 ARG cc_start: 0.8901 (ptp-170) cc_final: 0.8657 (ptp-170) REVERT: G 95 GLU cc_start: 0.8807 (mp0) cc_final: 0.8592 (mp0) REVERT: H 109 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8440 (mmtp) REVERT: H 119 ASN cc_start: 0.8465 (m110) cc_final: 0.8257 (m110) REVERT: I 92 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8260 (mp) REVERT: I 129 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8102 (ttm110) REVERT: K 119 ASN cc_start: 0.8489 (m110) cc_final: 0.8208 (m-40) REVERT: N 119 ASN cc_start: 0.8610 (m110) cc_final: 0.8387 (m-40) REVERT: Q 119 ASN cc_start: 0.8518 (m110) cc_final: 0.8298 (m-40) REVERT: R 119 ASN cc_start: 0.8562 (m110) cc_final: 0.8318 (m110) outliers start: 47 outliers final: 18 residues processed: 414 average time/residue: 0.3578 time to fit residues: 191.0811 Evaluate side-chains 379 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 360 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain D residue 105 LEU 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 Q residue 92 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain R residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 119 optimal weight: 0.0770 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 124 ASN J 124 ASN N 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107456 restraints weight = 14195.829| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.14 r_work: 0.3094 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12006 Z= 0.275 Angle : 0.594 5.053 16236 Z= 0.327 Chirality : 0.052 0.186 1836 Planarity : 0.004 0.037 2016 Dihedral : 4.532 23.459 1602 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.43 % Allowed : 25.90 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.21), residues: 1386 helix: -0.94 (0.39), residues: 180 sheet: -2.53 (0.19), residues: 594 loop : -2.05 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 123 HIS 0.004 0.002 HIS Q 139 PHE 0.023 0.002 PHE M 117 TYR 0.015 0.001 TYR K 160 ARG 0.008 0.001 ARG M 129 *********************** 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 396 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: B 109 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8341 (mmtp) REVERT: C 109 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8416 (mmtp) REVERT: C 122 GLU cc_start: 0.8397 (mp0) cc_final: 0.7961 (mp0) REVERT: D 164 ASP cc_start: 0.8729 (t0) cc_final: 0.8442 (t0) REVERT: E 119 ASN cc_start: 0.8489 (m110) cc_final: 0.8266 (m110) REVERT: E 122 GLU cc_start: 0.8105 (mp0) cc_final: 0.7699 (mp0) REVERT: E 164 ASP cc_start: 0.8763 (t0) cc_final: 0.8494 (t0) REVERT: H 109 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8355 (mmtp) REVERT: H 119 ASN cc_start: 0.8461 (m110) cc_final: 0.8221 (m110) REVERT: I 129 ARG cc_start: 0.8326 (ttm110) cc_final: 0.8121 (ttm110) REVERT: J 122 GLU cc_start: 0.8473 (mp0) cc_final: 0.7966 (mp0) REVERT: K 104 ARG cc_start: 0.7724 (mtt-85) cc_final: 0.7373 (mtp180) REVERT: N 119 ASN cc_start: 0.8554 (m110) cc_final: 0.8275 (m-40) REVERT: O 151 TYR cc_start: 0.9066 (m-80) cc_final: 0.8735 (m-80) REVERT: R 119 ASN cc_start: 0.8595 (m110) cc_final: 0.8246 (m110) outliers start: 31 outliers final: 19 residues processed: 388 average time/residue: 0.3375 time to fit residues: 170.0828 Evaluate side-chains 382 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 363 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 105 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain K residue 92 LEU 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 P residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 89 optimal weight: 0.0570 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 124 ASN C 106 ASN C 119 ASN C 124 ASN F 106 ASN G 106 ASN J 106 ASN J 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 = 0.3421 r_free = 0.3421 target = 0.123425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106474 restraints weight = 14187.602| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.07 r_work: 0.3078 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12006 Z= 0.303 Angle : 0.597 5.339 16236 Z= 0.329 Chirality : 0.052 0.191 1836 Planarity : 0.004 0.042 2016 Dihedral : 4.437 22.281 1602 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.30 % Allowed : 26.13 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.22), residues: 1386 helix: -0.87 (0.39), residues: 180 sheet: -2.19 (0.20), residues: 594 loop : -2.03 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 123 HIS 0.005 0.002 HIS R 139 PHE 0.019 0.002 PHE B 117 TYR 0.012 0.001 TYR I 160 ARG 0.009 0.001 ARG H 129 *********************** 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 419 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 364 time to evaluate : 1.255 Fit side-chains REVERT: C 109 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8455 (mmtp) REVERT: C 122 GLU cc_start: 0.8407 (mp0) cc_final: 0.7938 (mp0) REVERT: D 164 ASP cc_start: 0.8789 (t0) cc_final: 0.8248 (t0) REVERT: E 122 GLU cc_start: 0.8102 (mp0) cc_final: 0.7680 (mp0) REVERT: E 164 ASP cc_start: 0.8770 (t0) cc_final: 0.8234 (t0) REVERT: H 109 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8373 (mmtp) REVERT: H 119 ASN cc_start: 0.8561 (m110) cc_final: 0.8320 (m110) REVERT: I 107 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8513 (mtp-110) REVERT: I 110 THR cc_start: 0.8941 (m) cc_final: 0.8550 (p) REVERT: J 122 GLU cc_start: 0.8467 (mp0) cc_final: 0.8085 (mp0) REVERT: L 110 THR cc_start: 0.8887 (m) cc_final: 0.8562 (p) REVERT: N 119 ASN cc_start: 0.8552 (m110) cc_final: 0.8260 (m-40) REVERT: N 121 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7892 (ttpt) REVERT: O 151 TYR cc_start: 0.9066 (m-80) cc_final: 0.8755 (m-80) REVERT: Q 121 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8066 (ttpt) REVERT: R 104 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7416 (mtp180) REVERT: R 119 ASN cc_start: 0.8573 (m110) cc_final: 0.8210 (m110) outliers start: 55 outliers final: 32 residues processed: 406 average time/residue: 0.3272 time to fit residues: 173.5424 Evaluate side-chains 396 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 C residue 119 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 92 LEU 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 H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 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 119 ASN 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 O 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 105 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN C 119 ASN C 124 ASN D 124 ASN E 106 ASN H 124 ASN J 124 ASN M 124 ASN Q 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102350 restraints weight = 14992.852| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.37 r_work: 0.3022 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12006 Z= 0.356 Angle : 0.626 5.658 16236 Z= 0.344 Chirality : 0.054 0.218 1836 Planarity : 0.005 0.048 2016 Dihedral : 4.507 22.103 1602 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.85 % Allowed : 27.07 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.22), residues: 1386 helix: -0.82 (0.38), residues: 180 sheet: -2.12 (0.20), residues: 594 loop : -1.96 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 123 HIS 0.004 0.002 HIS G 139 PHE 0.022 0.002 PHE C 117 TYR 0.013 0.002 TYR J 151 ARG 0.010 0.001 ARG A 129 *********************** 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 435 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 373 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ASP cc_start: 0.9084 (t0) cc_final: 0.8526 (t0) REVERT: B 164 ASP cc_start: 0.8780 (t0) cc_final: 0.8455 (t0) REVERT: C 109 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8286 (mmtp) REVERT: C 122 GLU cc_start: 0.8487 (mp0) cc_final: 0.7998 (mp0) REVERT: D 164 ASP cc_start: 0.8852 (t0) cc_final: 0.8358 (t0) REVERT: E 115 MET cc_start: 0.9331 (mtp) cc_final: 0.9131 (mtm) REVERT: E 119 ASN cc_start: 0.8480 (m110) cc_final: 0.8189 (m110) REVERT: E 122 GLU cc_start: 0.8260 (mp0) cc_final: 0.7717 (mp0) REVERT: E 164 ASP cc_start: 0.8814 (t0) cc_final: 0.8327 (t0) REVERT: F 122 GLU cc_start: 0.8267 (mp0) cc_final: 0.7835 (mp0) REVERT: F 153 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8933 (mt) REVERT: G 121 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8530 (mtmm) REVERT: G 122 GLU cc_start: 0.8357 (mp0) cc_final: 0.7982 (mp0) REVERT: H 109 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8173 (mmtp) REVERT: H 119 ASN cc_start: 0.8626 (m110) cc_final: 0.8305 (m110) REVERT: H 122 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: H 153 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9026 (mt) REVERT: I 110 THR cc_start: 0.8972 (m) cc_final: 0.8550 (p) REVERT: I 121 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7659 (ttpp) REVERT: J 122 GLU cc_start: 0.8533 (mp0) cc_final: 0.8206 (mp0) REVERT: J 153 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9049 (mt) REVERT: K 104 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7348 (mtp180) REVERT: L 110 THR cc_start: 0.8951 (m) cc_final: 0.8598 (p) REVERT: M 110 THR cc_start: 0.8980 (m) cc_final: 0.8671 (p) REVERT: N 119 ASN cc_start: 0.8647 (m110) cc_final: 0.8262 (m-40) REVERT: Q 121 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8062 (ttpt) REVERT: R 110 THR cc_start: 0.8922 (m) cc_final: 0.8573 (p) REVERT: R 119 ASN cc_start: 0.8692 (m110) cc_final: 0.8287 (m110) REVERT: R 164 ASP cc_start: 0.8724 (t0) cc_final: 0.8458 (t0) outliers start: 62 outliers final: 32 residues processed: 423 average time/residue: 0.3171 time to fit residues: 176.5012 Evaluate side-chains 405 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 B residue 119 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 92 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 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 J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE 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 K residue 119 ASN 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 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 105 LEU 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 110 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN E 106 ASN J 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 = 0.3417 r_free = 0.3417 target = 0.122450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105030 restraints weight = 14964.287| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.35 r_work: 0.3060 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12006 Z= 0.257 Angle : 0.595 5.255 16236 Z= 0.326 Chirality : 0.052 0.212 1836 Planarity : 0.005 0.050 2016 Dihedral : 4.404 21.531 1602 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.63 % Allowed : 25.98 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.22), residues: 1386 helix: -0.71 (0.38), residues: 180 sheet: -2.04 (0.20), residues: 594 loop : -1.90 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 123 HIS 0.003 0.001 HIS R 139 PHE 0.016 0.002 PHE P 117 TYR 0.012 0.001 TYR M 160 ARG 0.010 0.001 ARG D 129 *********************** 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 426 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 354 time to evaluate : 1.294 Fit side-chains REVERT: A 95 GLU cc_start: 0.8924 (mp0) cc_final: 0.8723 (mp0) REVERT: A 122 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 109 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8232 (mmtp) REVERT: B 122 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: B 164 ASP cc_start: 0.8748 (t0) cc_final: 0.8385 (t0) REVERT: C 109 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8304 (mmtp) REVERT: C 122 GLU cc_start: 0.8464 (mp0) cc_final: 0.7979 (mp0) REVERT: D 95 GLU cc_start: 0.8881 (mp0) cc_final: 0.8133 (mp0) REVERT: D 122 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: E 122 GLU cc_start: 0.8246 (mp0) cc_final: 0.7715 (mp0) REVERT: E 153 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9008 (mt) REVERT: E 164 ASP cc_start: 0.8770 (t0) cc_final: 0.8463 (t0) REVERT: F 153 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8859 (mt) REVERT: G 122 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: H 109 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8219 (mmtp) REVERT: H 119 ASN cc_start: 0.8617 (m110) cc_final: 0.8322 (m110) REVERT: H 122 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: I 110 THR cc_start: 0.8947 (m) cc_final: 0.8520 (p) REVERT: J 110 THR cc_start: 0.8897 (m) cc_final: 0.8685 (t) REVERT: J 122 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: J 153 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8969 (mt) REVERT: L 110 THR cc_start: 0.8943 (m) cc_final: 0.8588 (p) REVERT: M 110 THR cc_start: 0.8965 (m) cc_final: 0.8615 (p) REVERT: N 119 ASN cc_start: 0.8633 (m110) cc_final: 0.8317 (m110) REVERT: N 121 LYS cc_start: 0.8296 (ttpt) cc_final: 0.7980 (ttpt) REVERT: O 151 TYR cc_start: 0.9055 (m-80) cc_final: 0.8731 (m-80) REVERT: P 92 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8063 (mp) REVERT: Q 121 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8129 (ttpt) REVERT: R 110 THR cc_start: 0.8958 (m) cc_final: 0.8572 (p) REVERT: R 119 ASN cc_start: 0.8611 (m110) cc_final: 0.8316 (m110) outliers start: 72 outliers final: 38 residues processed: 411 average time/residue: 0.3260 time to fit residues: 175.6093 Evaluate side-chains 400 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 352 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 119 ASN 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 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 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 102 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain O 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 100 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 112 optimal weight: 0.0670 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN E 106 ASN G 106 ASN H 124 ASN J 124 ASN L 106 ASN Q 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108730 restraints weight = 14742.005| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.39 r_work: 0.3111 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12006 Z= 0.178 Angle : 0.571 5.434 16236 Z= 0.310 Chirality : 0.051 0.183 1836 Planarity : 0.005 0.053 2016 Dihedral : 4.242 19.135 1602 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.69 % Allowed : 27.70 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.22), residues: 1386 helix: -0.62 (0.39), residues: 180 sheet: -2.03 (0.20), residues: 594 loop : -1.77 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 123 HIS 0.004 0.001 HIS Q 139 PHE 0.013 0.001 PHE P 117 TYR 0.013 0.001 TYR P 151 ARG 0.012 0.001 ARG H 129 *********************** 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 404 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 344 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: B 109 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8214 (mmtp) REVERT: B 122 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: B 153 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9017 (mt) REVERT: C 109 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8316 (mmtp) REVERT: C 122 GLU cc_start: 0.8469 (mp0) cc_final: 0.8016 (mp0) REVERT: D 95 GLU cc_start: 0.8853 (mp0) cc_final: 0.8183 (mp0) REVERT: D 122 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: E 122 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: F 122 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: F 153 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8866 (mt) REVERT: G 122 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: H 109 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8191 (mmtp) REVERT: H 122 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: J 122 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: J 153 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8957 (mt) REVERT: L 110 THR cc_start: 0.8928 (m) cc_final: 0.8558 (p) REVERT: M 110 THR cc_start: 0.8975 (m) cc_final: 0.8610 (p) REVERT: M 151 TYR cc_start: 0.8920 (m-80) cc_final: 0.8698 (m-80) REVERT: N 119 ASN cc_start: 0.8601 (m110) cc_final: 0.8299 (m110) REVERT: N 121 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7931 (ttpt) REVERT: P 92 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8053 (mp) REVERT: Q 121 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8004 (ttpt) REVERT: R 119 ASN cc_start: 0.8484 (m110) cc_final: 0.8193 (m110) outliers start: 60 outliers final: 28 residues processed: 395 average time/residue: 0.3130 time to fit residues: 163.3334 Evaluate side-chains 376 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 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 119 ASN Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 92 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 122 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 102 ILE 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 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 102 ILE Chi-restraints excluded: chain L 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 N residue 153 LEU Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 123 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN J 124 ASN K 124 ASN N 124 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102947 restraints weight = 15009.708| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.39 r_work: 0.3027 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12006 Z= 0.382 Angle : 0.649 5.548 16236 Z= 0.353 Chirality : 0.056 0.219 1836 Planarity : 0.006 0.061 2016 Dihedral : 4.470 21.388 1602 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.77 % Allowed : 26.68 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.22), residues: 1386 helix: -0.84 (0.37), residues: 180 sheet: -1.90 (0.20), residues: 594 loop : -1.79 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 123 HIS 0.004 0.002 HIS G 139 PHE 0.019 0.002 PHE C 117 TYR 0.016 0.002 TYR J 151 ARG 0.013 0.001 ARG H 129 *********************** 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 425 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 364 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: A 150 ARG cc_start: 0.8654 (mmt90) cc_final: 0.8441 (mmt90) REVERT: A 164 ASP cc_start: 0.8974 (t0) cc_final: 0.8428 (t0) REVERT: B 95 GLU cc_start: 0.8883 (mp0) cc_final: 0.8071 (mp0) REVERT: B 109 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8207 (mmtp) REVERT: B 122 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: B 153 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8908 (mt) REVERT: B 164 ASP cc_start: 0.8791 (t0) cc_final: 0.8256 (t0) REVERT: C 109 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8334 (mmtp) REVERT: C 122 GLU cc_start: 0.8503 (mp0) cc_final: 0.8021 (mp0) REVERT: D 95 GLU cc_start: 0.8975 (mp0) cc_final: 0.8242 (mp0) REVERT: D 122 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: D 164 ASP cc_start: 0.8629 (t0) cc_final: 0.8203 (t0) REVERT: E 122 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: E 164 ASP cc_start: 0.8798 (t70) cc_final: 0.8097 (t0) REVERT: F 121 LYS cc_start: 0.8525 (tptp) cc_final: 0.8115 (ttpt) REVERT: F 122 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: F 153 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8873 (mt) REVERT: G 122 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: H 109 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8188 (mmtp) REVERT: H 122 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: I 110 THR cc_start: 0.8964 (m) cc_final: 0.8528 (p) REVERT: J 122 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: J 153 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9063 (mt) REVERT: K 110 THR cc_start: 0.9005 (m) cc_final: 0.8647 (p) REVERT: K 121 LYS cc_start: 0.8504 (tptp) cc_final: 0.8288 (ttpp) REVERT: L 110 THR cc_start: 0.8936 (m) cc_final: 0.8600 (p) REVERT: M 110 THR cc_start: 0.8956 (m) cc_final: 0.8655 (p) REVERT: N 121 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8014 (ttpt) REVERT: O 110 THR cc_start: 0.8972 (m) cc_final: 0.8632 (p) REVERT: P 92 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8059 (mp) REVERT: P 164 ASP cc_start: 0.8862 (t0) cc_final: 0.8534 (t0) REVERT: Q 121 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8137 (ttpt) REVERT: Q 138 ASP cc_start: 0.8776 (t0) cc_final: 0.8425 (t0) REVERT: R 110 THR cc_start: 0.8953 (m) cc_final: 0.8625 (p) REVERT: R 119 ASN cc_start: 0.8669 (m110) cc_final: 0.8324 (m110) REVERT: R 164 ASP cc_start: 0.8827 (t0) cc_final: 0.8547 (t0) outliers start: 61 outliers final: 31 residues processed: 414 average time/residue: 0.3431 time to fit residues: 183.8773 Evaluate side-chains 404 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 361 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 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 119 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 119 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 122 GLU Chi-restraints excluded: chain F residue 92 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 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 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 102 ILE Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O 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 100 GLU Chi-restraints excluded: chain Q residue 105 LEU 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 58 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 124 ASN H 124 ASN J 124 ASN N 106 ASN N 124 ASN P 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103733 restraints weight = 14843.453| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.36 r_work: 0.3042 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12006 Z= 0.347 Angle : 0.649 5.897 16236 Z= 0.353 Chirality : 0.055 0.213 1836 Planarity : 0.006 0.065 2016 Dihedral : 4.544 20.638 1602 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.15 % Allowed : 28.17 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.22), residues: 1386 helix: -0.86 (0.37), residues: 180 sheet: -1.87 (0.20), residues: 594 loop : -1.79 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 123 HIS 0.004 0.001 HIS Q 139 PHE 0.015 0.002 PHE B 117 TYR 0.013 0.001 TYR J 151 ARG 0.014 0.002 ARG H 129 *********************** 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 404 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 351 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7699 (ttpp) REVERT: A 122 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 164 ASP cc_start: 0.8975 (t0) cc_final: 0.8285 (t0) REVERT: B 95 GLU cc_start: 0.8898 (mp0) cc_final: 0.8093 (mp0) REVERT: B 109 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8227 (mmtp) REVERT: B 122 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: B 153 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9010 (mt) REVERT: B 164 ASP cc_start: 0.8774 (t0) cc_final: 0.8231 (t0) REVERT: C 109 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8323 (mmtp) REVERT: C 122 GLU cc_start: 0.8466 (mp0) cc_final: 0.7963 (mp0) REVERT: D 95 GLU cc_start: 0.8934 (mp0) cc_final: 0.8166 (mp0) REVERT: D 122 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: D 164 ASP cc_start: 0.8633 (t0) cc_final: 0.8202 (t0) REVERT: E 122 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: E 164 ASP cc_start: 0.8755 (t70) cc_final: 0.8078 (t0) REVERT: F 95 GLU cc_start: 0.8889 (mp0) cc_final: 0.8613 (mp0) REVERT: F 121 LYS cc_start: 0.8517 (tptp) cc_final: 0.8124 (ttpt) REVERT: F 122 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: F 153 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8913 (mt) REVERT: G 122 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: H 109 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8214 (mmtp) REVERT: H 122 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: I 110 THR cc_start: 0.8966 (m) cc_final: 0.8537 (p) REVERT: J 122 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: J 153 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8985 (mt) REVERT: K 110 THR cc_start: 0.8996 (m) cc_final: 0.8650 (p) REVERT: K 121 LYS cc_start: 0.8467 (tptp) cc_final: 0.8243 (ttpp) REVERT: L 110 THR cc_start: 0.8943 (m) cc_final: 0.8597 (p) REVERT: L 164 ASP cc_start: 0.8704 (t0) cc_final: 0.8487 (t0) REVERT: M 110 THR cc_start: 0.8962 (m) cc_final: 0.8665 (p) REVERT: N 121 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8119 (ttpt) REVERT: O 110 THR cc_start: 0.8986 (m) cc_final: 0.8647 (p) REVERT: P 92 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8084 (mp) REVERT: P 164 ASP cc_start: 0.8902 (t0) cc_final: 0.8573 (t0) REVERT: Q 121 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8132 (ttpt) REVERT: Q 138 ASP cc_start: 0.8831 (t0) cc_final: 0.8416 (t0) REVERT: R 110 THR cc_start: 0.8941 (m) cc_final: 0.8620 (p) REVERT: R 119 ASN cc_start: 0.8685 (m110) cc_final: 0.8350 (m110) REVERT: R 164 ASP cc_start: 0.8859 (t0) cc_final: 0.8386 (t0) outliers start: 53 outliers final: 34 residues processed: 390 average time/residue: 0.3394 time to fit residues: 170.4540 Evaluate side-chains 395 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 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 119 ASN 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 119 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 122 GLU Chi-restraints excluded: chain F residue 92 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 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 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 K residue 119 ASN Chi-restraints excluded: chain L 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 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 100 GLU Chi-restraints excluded: chain Q residue 105 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 12 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 0.0000 chunk 85 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN J 124 ASN N 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108650 restraints weight = 14470.583| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.33 r_work: 0.3119 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12006 Z= 0.183 Angle : 0.606 6.752 16236 Z= 0.328 Chirality : 0.051 0.190 1836 Planarity : 0.006 0.063 2016 Dihedral : 4.370 18.452 1602 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.60 % Allowed : 28.40 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1386 helix: -0.64 (0.38), residues: 180 sheet: -1.52 (0.21), residues: 504 loop : -1.80 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 123 HIS 0.004 0.001 HIS Q 139 PHE 0.013 0.001 PHE O 117 TYR 0.012 0.001 TYR L 114 ARG 0.014 0.002 ARG D 129 ********************** 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 390 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7675 (ttpp) REVERT: A 122 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: B 95 GLU cc_start: 0.8813 (mp0) cc_final: 0.8039 (mp0) REVERT: B 109 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8223 (mmtp) REVERT: B 122 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: B 153 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8874 (mt) REVERT: C 109 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8323 (mmtp) REVERT: C 122 GLU cc_start: 0.8490 (mp0) cc_final: 0.8043 (mp0) REVERT: D 95 GLU cc_start: 0.8845 (mp0) cc_final: 0.8122 (mp0) REVERT: D 122 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: E 122 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: E 153 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8929 (mt) REVERT: F 95 GLU cc_start: 0.8818 (mp0) cc_final: 0.8530 (mp0) REVERT: F 122 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: F 153 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8843 (mt) REVERT: G 122 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: H 109 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8199 (mmtp) REVERT: H 122 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: I 110 THR cc_start: 0.8935 (m) cc_final: 0.8471 (p) REVERT: J 122 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: L 110 THR cc_start: 0.8926 (m) cc_final: 0.8559 (p) REVERT: N 121 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7925 (ttpt) REVERT: O 151 TYR cc_start: 0.8994 (m-80) cc_final: 0.8764 (m-80) REVERT: P 92 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (mp) REVERT: Q 121 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7684 (ttpt) REVERT: Q 122 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: Q 138 ASP cc_start: 0.8812 (t0) cc_final: 0.8371 (t0) REVERT: R 110 THR cc_start: 0.8956 (m) cc_final: 0.8592 (p) REVERT: R 119 ASN cc_start: 0.8518 (m110) cc_final: 0.8259 (m110) REVERT: R 164 ASP cc_start: 0.8698 (t0) cc_final: 0.8374 (t0) outliers start: 46 outliers final: 24 residues processed: 383 average time/residue: 0.3165 time to fit residues: 159.4956 Evaluate side-chains 376 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 339 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU 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 92 LEU 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 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 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 102 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 122 GLU 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 82 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 0.0570 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN D 124 ASN H 124 ASN J 124 ASN N 124 ASN O 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109239 restraints weight = 14387.285| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.35 r_work: 0.3125 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12006 Z= 0.185 Angle : 0.598 6.322 16236 Z= 0.323 Chirality : 0.052 0.193 1836 Planarity : 0.006 0.064 2016 Dihedral : 4.251 17.347 1602 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.60 % Allowed : 29.11 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.22), residues: 1386 helix: -0.49 (0.39), residues: 180 sheet: -1.39 (0.21), residues: 504 loop : -1.64 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 123 HIS 0.004 0.001 HIS Q 139 PHE 0.012 0.001 PHE O 117 TYR 0.012 0.001 TYR L 114 ARG 0.014 0.002 ARG R 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5805.44 seconds wall clock time: 104 minutes 31.23 seconds (6271.23 seconds total)