Starting phenix.real_space_refine on Sat Nov 16 18:19:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zra_60394/11_2024/8zra_60394.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zra_60394/11_2024/8zra_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zra_60394/11_2024/8zra_60394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zra_60394/11_2024/8zra_60394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zra_60394/11_2024/8zra_60394.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zra_60394/11_2024/8zra_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.47, per 1000 atoms: 0.29 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: 3.20 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: 1.72 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: 3.06 Time building geometry restraints manager: 3.65 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 25.130 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- 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 : 1.510 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: 0.4065 time to fit residues: 208.3737 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 : 1.382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 1.954 Fit side-chains revert: symmetry clash REVERT: B 109 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8175 (mmtp) REVERT: B 119 ASN cc_start: 0.8120 (m110) cc_final: 0.7850 (m-40) REVERT: C 109 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8283 (mmtp) REVERT: E 109 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8224 (mmtp) REVERT: E 119 ASN cc_start: 0.8065 (m110) cc_final: 0.7775 (m-40) REVERT: E 164 ASP cc_start: 0.8539 (t0) cc_final: 0.8100 (t0) REVERT: F 137 ARG cc_start: 0.8800 (ptp-170) cc_final: 0.8560 (ptp-170) REVERT: H 109 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8189 (mmtp) REVERT: H 119 ASN cc_start: 0.8059 (m110) cc_final: 0.7855 (m110) REVERT: H 159 ASP cc_start: 0.8527 (m-30) cc_final: 0.8224 (m-30) REVERT: H 164 ASP cc_start: 0.8444 (t0) cc_final: 0.8242 (t0) REVERT: I 92 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8097 (mp) REVERT: K 119 ASN cc_start: 0.8190 (m110) cc_final: 0.7890 (m-40) REVERT: K 164 ASP cc_start: 0.8300 (t70) cc_final: 0.8100 (t0) REVERT: N 119 ASN cc_start: 0.8180 (m110) cc_final: 0.7952 (m-40) REVERT: N 159 ASP cc_start: 0.8543 (m-30) cc_final: 0.8318 (m-30) REVERT: Q 119 ASN cc_start: 0.8134 (m110) cc_final: 0.7909 (m-40) REVERT: R 119 ASN cc_start: 0.8234 (m110) cc_final: 0.7982 (m110) outliers start: 47 outliers final: 18 residues processed: 414 average time/residue: 0.3749 time to fit residues: 203.3684 Evaluate side-chains 380 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 361 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN J 124 ASN N 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12006 Z= 0.146 Angle : 0.540 4.737 16236 Z= 0.296 Chirality : 0.049 0.147 1836 Planarity : 0.004 0.038 2016 Dihedral : 4.393 22.213 1602 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.88 % Allowed : 25.98 % Favored : 72.14 % 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: -3.35 (0.22), residues: 1386 helix: -0.77 (0.41), residues: 180 sheet: -2.47 (0.19), residues: 702 loop : -2.01 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 123 HIS 0.002 0.001 HIS O 139 PHE 0.017 0.002 PHE M 117 TYR 0.015 0.001 TYR P 160 ARG 0.009 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 370 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 346 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: B 109 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8225 (mmtp) REVERT: C 109 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8226 (mmtp) REVERT: E 109 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8156 (mmtp) REVERT: H 109 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8142 (mmtp) REVERT: M 151 TYR cc_start: 0.8591 (m-80) cc_final: 0.8372 (m-80) REVERT: O 151 TYR cc_start: 0.8642 (m-80) cc_final: 0.8389 (m-80) REVERT: Q 137 ARG cc_start: 0.8389 (ptp-170) cc_final: 0.8115 (ptp-170) REVERT: R 119 ASN cc_start: 0.8091 (m110) cc_final: 0.7808 (m110) outliers start: 24 outliers final: 12 residues processed: 363 average time/residue: 0.3500 time to fit residues: 166.2197 Evaluate side-chains 351 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 339 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 102 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain R residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 106 ASN J 106 ASN J 124 ASN Q 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12006 Z= 0.439 Angle : 0.653 5.206 16236 Z= 0.360 Chirality : 0.055 0.202 1836 Planarity : 0.005 0.041 2016 Dihedral : 4.554 22.316 1602 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.60 % Allowed : 26.45 % Favored : 69.95 % 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: -3.09 (0.22), residues: 1386 helix: -0.97 (0.38), residues: 180 sheet: -2.16 (0.20), residues: 594 loop : -2.09 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 123 HIS 0.006 0.003 HIS F 139 PHE 0.023 0.003 PHE H 117 TYR 0.015 0.002 TYR J 151 ARG 0.010 0.001 ARG R 104 *********************** 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 422 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 376 time to evaluate : 1.429 Fit side-chains REVERT: A 122 GLU cc_start: 0.7701 (mp0) cc_final: 0.7249 (mp0) REVERT: B 115 MET cc_start: 0.8902 (mtp) cc_final: 0.8561 (ttm) REVERT: B 164 ASP cc_start: 0.8567 (t0) cc_final: 0.8300 (t0) REVERT: C 109 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8234 (mmtp) REVERT: C 122 GLU cc_start: 0.7794 (mp0) cc_final: 0.7152 (mp0) REVERT: C 164 ASP cc_start: 0.8614 (t0) cc_final: 0.7932 (t0) REVERT: D 164 ASP cc_start: 0.8584 (t0) cc_final: 0.8307 (t0) REVERT: E 122 GLU cc_start: 0.7695 (mp0) cc_final: 0.7239 (mp0) REVERT: E 164 ASP cc_start: 0.8594 (t70) cc_final: 0.7921 (t0) REVERT: F 164 ASP cc_start: 0.8621 (t0) cc_final: 0.8135 (t0) REVERT: G 122 GLU cc_start: 0.7763 (mp0) cc_final: 0.6607 (mp0) REVERT: H 109 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8116 (mmtp) REVERT: H 164 ASP cc_start: 0.8684 (t70) cc_final: 0.8244 (t0) REVERT: I 92 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8137 (mt) REVERT: I 110 THR cc_start: 0.8882 (m) cc_final: 0.8458 (p) REVERT: J 122 GLU cc_start: 0.7875 (mp0) cc_final: 0.7470 (mp0) REVERT: K 164 ASP cc_start: 0.8415 (t70) cc_final: 0.8186 (t0) REVERT: L 110 THR cc_start: 0.8929 (m) cc_final: 0.8571 (p) REVERT: M 110 THR cc_start: 0.8923 (m) cc_final: 0.8553 (p) REVERT: R 110 THR cc_start: 0.8856 (m) cc_final: 0.8509 (p) REVERT: R 119 ASN cc_start: 0.8151 (m110) cc_final: 0.7797 (m110) REVERT: R 164 ASP cc_start: 0.8621 (t70) cc_final: 0.8191 (t0) outliers start: 46 outliers final: 25 residues processed: 410 average time/residue: 0.3417 time to fit residues: 181.5340 Evaluate side-chains 399 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 373 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 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 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 G residue 92 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I 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 M residue 92 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN E 106 ASN J 124 ASN Q 106 ASN Q 124 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12006 Z= 0.251 Angle : 0.587 5.281 16236 Z= 0.323 Chirality : 0.052 0.190 1836 Planarity : 0.005 0.046 2016 Dihedral : 4.384 21.668 1602 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.60 % Allowed : 28.56 % Favored : 67.84 % 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: -0.70 (0.39), residues: 180 sheet: -2.14 (0.20), residues: 594 loop : -1.98 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 123 HIS 0.003 0.002 HIS P 139 PHE 0.019 0.002 PHE H 117 TYR 0.013 0.001 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 408 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 362 time to evaluate : 1.451 Fit side-chains REVERT: A 129 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7339 (ttm110) REVERT: B 109 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8172 (mmtp) REVERT: B 164 ASP cc_start: 0.8519 (t0) cc_final: 0.8212 (t0) REVERT: C 109 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8234 (mmtp) REVERT: C 122 GLU cc_start: 0.7766 (mp0) cc_final: 0.7320 (mp0) REVERT: D 122 GLU cc_start: 0.7717 (mp0) cc_final: 0.7164 (mp0) REVERT: D 153 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8629 (mt) REVERT: D 164 ASP cc_start: 0.8623 (t0) cc_final: 0.8326 (t0) REVERT: E 103 LEU cc_start: 0.8339 (mt) cc_final: 0.8062 (mt) REVERT: E 122 GLU cc_start: 0.7657 (mp0) cc_final: 0.7181 (mp0) REVERT: E 164 ASP cc_start: 0.8507 (t70) cc_final: 0.7782 (t0) REVERT: G 122 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: H 109 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8090 (mmtp) REVERT: H 115 MET cc_start: 0.8833 (mtp) cc_final: 0.8588 (ttm) REVERT: H 122 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: H 153 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8814 (mt) REVERT: H 164 ASP cc_start: 0.8636 (t70) cc_final: 0.8174 (t0) REVERT: I 121 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7533 (ttpt) REVERT: J 122 GLU cc_start: 0.7839 (mp0) cc_final: 0.7392 (mp0) REVERT: K 164 ASP cc_start: 0.8344 (t70) cc_final: 0.8118 (t0) REVERT: L 121 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8440 (pttp) REVERT: Q 121 LYS cc_start: 0.8298 (ttpt) cc_final: 0.8005 (ttpt) REVERT: R 164 ASP cc_start: 0.8562 (t70) cc_final: 0.8283 (t0) outliers start: 46 outliers final: 23 residues processed: 398 average time/residue: 0.3061 time to fit residues: 158.7414 Evaluate side-chains 389 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 362 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE 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 K residue 92 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 119 ASN 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 106 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN J 124 ASN Q 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12006 Z= 0.217 Angle : 0.574 5.521 16236 Z= 0.313 Chirality : 0.051 0.177 1836 Planarity : 0.005 0.050 2016 Dihedral : 4.227 20.260 1602 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.01 % Allowed : 27.62 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.76 (0.22), residues: 1386 helix: -0.44 (0.39), residues: 180 sheet: -2.04 (0.20), residues: 594 loop : -1.87 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 123 HIS 0.003 0.001 HIS O 139 PHE 0.015 0.002 PHE P 117 TYR 0.013 0.001 TYR Q 160 ARG 0.011 0.001 ARG H 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 405 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 341 time to evaluate : 1.471 Fit side-chains REVERT: B 109 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8165 (mmtp) REVERT: B 122 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: C 109 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8188 (mmtp) REVERT: C 122 GLU cc_start: 0.7793 (mp0) cc_final: 0.7367 (mp0) REVERT: D 122 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: D 153 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8639 (mt) REVERT: E 115 MET cc_start: 0.8813 (mtp) cc_final: 0.8591 (mtm) REVERT: E 153 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8634 (mt) REVERT: E 164 ASP cc_start: 0.8489 (t70) cc_final: 0.7750 (t0) REVERT: G 122 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: H 109 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8091 (mmtp) REVERT: H 115 MET cc_start: 0.8857 (mtp) cc_final: 0.8565 (ttm) REVERT: H 122 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: H 153 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8810 (mt) REVERT: H 164 ASP cc_start: 0.8563 (t70) cc_final: 0.8100 (t0) REVERT: I 92 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7944 (mt) REVERT: J 122 GLU cc_start: 0.7843 (mp0) cc_final: 0.7406 (mp0) REVERT: J 153 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8812 (mt) REVERT: L 110 THR cc_start: 0.8896 (m) cc_final: 0.8521 (p) REVERT: L 121 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8414 (pttp) REVERT: O 151 TYR cc_start: 0.8739 (m-80) cc_final: 0.8402 (m-80) REVERT: Q 121 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7943 (ttpt) REVERT: R 164 ASP cc_start: 0.8501 (t70) cc_final: 0.8205 (t0) outliers start: 64 outliers final: 29 residues processed: 395 average time/residue: 0.3297 time to fit residues: 171.7772 Evaluate side-chains 378 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 B residue 105 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 102 ILE 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 H residue 153 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 115 MET 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 102 ILE Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.0270 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN E 106 ASN J 124 ASN L 106 ASN N 124 ASN Q 106 ASN R 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12006 Z= 0.335 Angle : 0.623 5.651 16236 Z= 0.341 Chirality : 0.054 0.201 1836 Planarity : 0.005 0.056 2016 Dihedral : 4.373 20.372 1602 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.48 % Allowed : 27.39 % Favored : 67.14 % 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: -0.60 (0.38), residues: 180 sheet: -1.95 (0.20), residues: 594 loop : -1.81 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 123 HIS 0.004 0.002 HIS J 139 PHE 0.018 0.002 PHE H 117 TYR 0.014 0.001 TYR J 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 432 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 362 time to evaluate : 1.353 Fit side-chains REVERT: A 122 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: A 164 ASP cc_start: 0.8658 (t0) cc_final: 0.8112 (t0) REVERT: B 109 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8196 (mmtp) REVERT: B 122 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: B 153 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8744 (mt) REVERT: C 109 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8240 (mmtp) REVERT: C 122 GLU cc_start: 0.7810 (mp0) cc_final: 0.7357 (mp0) REVERT: D 122 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: D 164 ASP cc_start: 0.8471 (t0) cc_final: 0.8185 (t0) REVERT: E 115 MET cc_start: 0.8799 (mtp) cc_final: 0.8587 (mtm) REVERT: E 122 GLU cc_start: 0.7714 (mp0) cc_final: 0.7223 (mp0) REVERT: E 153 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8696 (mt) REVERT: E 164 ASP cc_start: 0.8563 (t70) cc_final: 0.7872 (t0) REVERT: G 122 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: H 109 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8073 (mmtp) REVERT: H 115 MET cc_start: 0.8918 (mtp) cc_final: 0.8685 (ttm) REVERT: H 122 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: H 153 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8828 (mt) REVERT: H 159 ASP cc_start: 0.8590 (m-30) cc_final: 0.8370 (m-30) REVERT: H 164 ASP cc_start: 0.8650 (t70) cc_final: 0.8223 (t0) REVERT: I 92 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7946 (mt) REVERT: J 122 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: J 153 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8822 (mt) REVERT: L 110 THR cc_start: 0.8896 (m) cc_final: 0.8546 (p) REVERT: L 121 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8484 (pttp) REVERT: M 110 THR cc_start: 0.8902 (m) cc_final: 0.8576 (p) REVERT: P 92 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7956 (mp) REVERT: P 164 ASP cc_start: 0.8665 (t0) cc_final: 0.8376 (t0) REVERT: Q 121 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7968 (ttpt) REVERT: R 110 THR cc_start: 0.8906 (m) cc_final: 0.8548 (p) REVERT: R 164 ASP cc_start: 0.8544 (t70) cc_final: 0.8068 (t0) outliers start: 70 outliers final: 34 residues processed: 417 average time/residue: 0.3256 time to fit residues: 177.6884 Evaluate side-chains 404 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 358 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 122 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 105 LEU 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 D residue 92 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 119 ASN 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 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 H residue 153 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 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 105 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 119 ASN 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 92 LEU 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 Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN G 106 ASN J 124 ASN Q 106 ASN R 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3217 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= 0.322 Angle : 0.625 5.736 16236 Z= 0.341 Chirality : 0.054 0.227 1836 Planarity : 0.006 0.060 2016 Dihedral : 4.402 19.678 1602 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.56 % Allowed : 27.39 % Favored : 67.06 % 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: -2.64 (0.22), residues: 1386 helix: -0.63 (0.37), residues: 180 sheet: -1.91 (0.20), residues: 594 loop : -1.76 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 123 HIS 0.004 0.001 HIS J 139 PHE 0.015 0.002 PHE H 117 TYR 0.013 0.001 TYR J 151 ARG 0.013 0.002 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 431 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 360 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7671 (ttpp) REVERT: A 122 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 164 ASP cc_start: 0.8686 (t0) cc_final: 0.8122 (t0) REVERT: B 109 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8172 (mmtp) REVERT: B 122 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 153 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8753 (mt) REVERT: C 109 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8201 (mmtp) REVERT: C 122 GLU cc_start: 0.7825 (mp0) cc_final: 0.7366 (mp0) REVERT: D 122 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: E 115 MET cc_start: 0.8798 (mtp) cc_final: 0.8587 (mtm) REVERT: E 122 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: E 153 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8690 (mt) REVERT: E 164 ASP cc_start: 0.8548 (t70) cc_final: 0.7863 (t0) REVERT: F 122 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: G 95 GLU cc_start: 0.8885 (mp0) cc_final: 0.8565 (mp0) REVERT: G 122 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: H 109 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8067 (mmtp) REVERT: H 115 MET cc_start: 0.8918 (mtp) cc_final: 0.8672 (ttm) REVERT: H 122 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: H 153 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8829 (mt) REVERT: H 164 ASP cc_start: 0.8631 (t70) cc_final: 0.8211 (t0) REVERT: I 92 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7934 (mt) REVERT: I 150 ARG cc_start: 0.8407 (mtt90) cc_final: 0.8100 (mpt-90) REVERT: J 122 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: J 153 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8813 (mt) REVERT: L 110 THR cc_start: 0.8895 (m) cc_final: 0.8537 (p) REVERT: M 110 THR cc_start: 0.8907 (m) cc_final: 0.8566 (p) REVERT: P 92 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7983 (mp) REVERT: P 164 ASP cc_start: 0.8642 (t0) cc_final: 0.8347 (t0) REVERT: Q 121 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7992 (ttpt) REVERT: R 110 THR cc_start: 0.8896 (m) cc_final: 0.8541 (p) REVERT: R 164 ASP cc_start: 0.8539 (t70) cc_final: 0.8061 (t0) outliers start: 71 outliers final: 39 residues processed: 412 average time/residue: 0.3355 time to fit residues: 180.2462 Evaluate side-chains 410 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 357 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 105 LEU 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 106 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain 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 K residue 119 ASN Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 119 ASN 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 92 LEU 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 Q residue 106 ASN Chi-restraints excluded: chain R residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN G 106 ASN J 124 ASN N 124 ASN Q 106 ASN R 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12006 Z= 0.198 Angle : 0.594 5.904 16236 Z= 0.322 Chirality : 0.052 0.204 1836 Planarity : 0.006 0.061 2016 Dihedral : 4.253 18.019 1602 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.99 % Allowed : 29.11 % Favored : 66.90 % 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: -2.62 (0.22), residues: 1386 helix: -0.60 (0.38), residues: 180 sheet: -1.93 (0.20), residues: 594 loop : -1.70 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 123 HIS 0.004 0.001 HIS Q 139 PHE 0.013 0.001 PHE P 117 TYR 0.014 0.001 TYR J 151 ARG 0.014 0.002 ARG D 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 389 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 338 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: B 95 GLU cc_start: 0.8850 (mp0) cc_final: 0.8218 (mp0) REVERT: B 109 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8186 (mmtp) REVERT: B 122 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: B 153 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8653 (mt) REVERT: C 109 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8180 (mmtp) REVERT: C 122 GLU cc_start: 0.7811 (mp0) cc_final: 0.7376 (mp0) REVERT: D 95 GLU cc_start: 0.8778 (mp0) cc_final: 0.8061 (mp0) REVERT: D 122 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: E 109 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8067 (mmtp) REVERT: E 122 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: E 153 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8694 (mt) REVERT: E 164 ASP cc_start: 0.8474 (t70) cc_final: 0.7959 (t0) REVERT: F 95 GLU cc_start: 0.8808 (mp0) cc_final: 0.8568 (mp0) REVERT: F 122 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: G 95 GLU cc_start: 0.8879 (mp0) cc_final: 0.8575 (mp0) REVERT: H 109 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8121 (mmtp) REVERT: H 122 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: H 153 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8841 (mt) REVERT: H 164 ASP cc_start: 0.8491 (t70) cc_final: 0.8033 (t0) REVERT: J 122 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: J 153 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8864 (mt) REVERT: L 104 ARG cc_start: 0.6965 (mtt-85) cc_final: 0.6721 (mtp180) REVERT: L 110 THR cc_start: 0.8884 (m) cc_final: 0.8503 (p) REVERT: L 121 LYS cc_start: 0.8695 (mmtm) cc_final: 0.8398 (ttpt) REVERT: M 110 THR cc_start: 0.8933 (m) cc_final: 0.8554 (p) REVERT: O 151 TYR cc_start: 0.8723 (m-80) cc_final: 0.8435 (m-80) REVERT: P 92 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7984 (mp) REVERT: Q 121 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7919 (ttpt) REVERT: R 110 THR cc_start: 0.8916 (m) cc_final: 0.8514 (p) REVERT: R 164 ASP cc_start: 0.8447 (t70) cc_final: 0.8154 (t0) outliers start: 51 outliers final: 29 residues processed: 381 average time/residue: 0.3217 time to fit residues: 159.6876 Evaluate side-chains 375 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 334 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain 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 G residue 92 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 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 P residue 92 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 0.0070 chunk 77 optimal weight: 0.0020 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN B 124 ASN C 106 ASN C 124 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN J 124 ASN N 124 ASN O 124 ASN Q 106 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3636 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= 0.163 Angle : 0.578 5.662 16236 Z= 0.311 Chirality : 0.050 0.168 1836 Planarity : 0.006 0.063 2016 Dihedral : 4.138 17.207 1602 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.44 % Allowed : 29.66 % Favored : 66.90 % 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: -2.27 (0.22), residues: 1386 helix: -0.46 (0.39), residues: 180 sheet: -1.54 (0.21), residues: 504 loop : -1.70 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 123 HIS 0.003 0.001 HIS Q 139 PHE 0.011 0.001 PHE O 117 TYR 0.012 0.001 TYR Q 160 ARG 0.014 0.002 ARG R 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 386 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: B 95 GLU cc_start: 0.8733 (mp0) cc_final: 0.8202 (mp0) REVERT: B 109 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8055 (mmtp) REVERT: B 122 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 153 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8715 (mt) REVERT: C 109 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8193 (mmtp) REVERT: C 122 GLU cc_start: 0.7742 (mp0) cc_final: 0.7470 (mp0) REVERT: D 95 GLU cc_start: 0.8817 (mp0) cc_final: 0.8150 (mp0) REVERT: D 122 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: E 109 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8022 (mmtp) REVERT: E 122 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: F 122 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: G 95 GLU cc_start: 0.8840 (mp0) cc_final: 0.8533 (mp0) REVERT: G 109 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8153 (mmtm) REVERT: G 122 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: H 109 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8098 (mmtp) REVERT: H 115 MET cc_start: 0.8734 (mtp) cc_final: 0.8527 (ttm) REVERT: H 122 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: I 107 ARG cc_start: 0.8562 (mtp-110) cc_final: 0.8295 (mtp-110) REVERT: I 121 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7911 (ttpt) REVERT: J 122 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: L 110 THR cc_start: 0.8837 (m) cc_final: 0.8456 (p) REVERT: L 121 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8341 (ttpp) REVERT: O 151 TYR cc_start: 0.8707 (m-80) cc_final: 0.8461 (m-80) REVERT: Q 121 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7861 (ttpt) REVERT: Q 138 ASP cc_start: 0.8314 (t0) cc_final: 0.7910 (t0) REVERT: R 110 THR cc_start: 0.8899 (m) cc_final: 0.8494 (p) outliers start: 44 outliers final: 20 residues processed: 376 average time/residue: 0.3266 time to fit residues: 160.6064 Evaluate side-chains 368 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 339 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 122 GLU 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 106 ASN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 92 LEU 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 L residue 102 ILE Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain Q residue 106 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 2.5544 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 106 ASN J 124 ASN N 124 ASN P 124 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 = 0.3426 r_free = 0.3426 target = 0.122805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105644 restraints weight = 14597.166| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.33 r_work: 0.3067 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12006 Z= 0.317 Angle : 0.626 7.209 16236 Z= 0.338 Chirality : 0.055 0.202 1836 Planarity : 0.006 0.067 2016 Dihedral : 4.271 17.398 1602 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.97 % Allowed : 29.97 % Favored : 67.06 % 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: -2.33 (0.22), residues: 1386 helix: -0.46 (0.39), residues: 180 sheet: -1.71 (0.20), residues: 594 loop : -1.53 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 123 HIS 0.003 0.001 HIS N 139 PHE 0.018 0.002 PHE J 128 TYR 0.013 0.001 TYR J 151 ARG 0.014 0.002 ARG H 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.36 seconds wall clock time: 67 minutes 53.99 seconds (4073.99 seconds total)