Starting phenix.real_space_refine on Sat Jul 4 05:31:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzx_33533/07_2026/7xzx_33533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzx_33533/07_2026/7xzx_33533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xzx_33533/07_2026/7xzx_33533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzx_33533/07_2026/7xzx_33533.map" model { file = "/net/cci-nas-00/data/ceres_data/7xzx_33533/07_2026/7xzx_33533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzx_33533/07_2026/7xzx_33533.cif" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 341 5.49 5 S 78 5.16 5 C 10946 2.51 5 N 3618 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19270 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3487 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3507 Classifications: {'DNA': 171} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 170} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "L" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "M" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "N" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Time building chain proxies: 3.99, per 1000 atoms: 0.21 Number of scatterers: 19270 At special positions: 0 Unit cell: (170.5, 157.3, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 341 15.00 O 4287 8.00 N 3618 7.00 C 10946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 661.6 milliseconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 42.9% alpha, 15.2% beta 166 base pairs and 300 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.292A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.117A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.994A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.537A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.267A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.523A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 288 Processing helix chain 'K' and resid 289 through 291 No H-bonds generated for 'chain 'K' and resid 289 through 291' Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 277 through 288 Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 289 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 288 Processing helix chain 'N' and resid 289 through 291 No H-bonds generated for 'chain 'N' and resid 289 through 291' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.083A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.757A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.760A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.547A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 6.213A pdb=" N LEU K 257 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG K 267 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE K 255 " --> pdb=" O ARG K 267 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER K 269 " --> pdb=" O THR K 253 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR K 253 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE K 251 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.802A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.832A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.840A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 854 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 300 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3653 1.33 - 1.46: 6944 1.46 - 1.59: 8955 1.59 - 1.71: 679 1.71 - 1.84: 112 Bond restraints: 20343 Sorted by residual: bond pdb=" C1' DT J 163 " pdb=" N1 DT J 163 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" C1' DA I 31 " pdb=" N9 DA I 31 " ideal model delta sigma weight residual 1.468 1.405 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" C3' DC I 145 " pdb=" C2' DC I 145 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.52e+01 bond pdb=" C PRO L 222 " pdb=" O PRO L 222 " ideal model delta sigma weight residual 1.246 1.213 0.033 8.50e-03 1.38e+04 1.48e+01 bond pdb=" C3' DC I 34 " pdb=" C2' DC I 34 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 ... (remaining 20338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 26287 1.73 - 3.47: 2350 3.47 - 5.20: 249 5.20 - 6.93: 69 6.93 - 8.66: 3 Bond angle restraints: 28958 Sorted by residual: angle pdb=" O4' DA J 114 " pdb=" C1' DA J 114 " pdb=" N9 DA J 114 " ideal model delta sigma weight residual 108.00 112.08 -4.08 7.00e-01 2.04e+00 3.40e+01 angle pdb=" O5' DC I 168 " pdb=" C5' DC I 168 " pdb=" C4' DC I 168 " ideal model delta sigma weight residual 109.40 113.42 -4.02 8.00e-01 1.56e+00 2.52e+01 angle pdb=" O4' DC J 73 " pdb=" C1' DC J 73 " pdb=" N1 DC J 73 " ideal model delta sigma weight residual 108.00 111.48 -3.48 7.00e-01 2.04e+00 2.47e+01 angle pdb=" C3' DA I 17 " pdb=" C2' DA I 17 " pdb=" C1' DA I 17 " ideal model delta sigma weight residual 102.50 96.58 5.92 1.20e+00 6.94e-01 2.43e+01 angle pdb=" C3' DA I 155 " pdb=" C2' DA I 155 " pdb=" C1' DA I 155 " ideal model delta sigma weight residual 102.50 96.58 5.92 1.20e+00 6.94e-01 2.43e+01 ... (remaining 28953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 9312 30.70 - 61.41: 2035 61.41 - 92.11: 63 92.11 - 122.81: 1 122.81 - 153.51: 1 Dihedral angle restraints: 11412 sinusoidal: 6908 harmonic: 4504 Sorted by residual: dihedral pdb=" C4' DC J 33 " pdb=" C3' DC J 33 " pdb=" O3' DC J 33 " pdb=" P DC J 34 " ideal model delta sinusoidal sigma weight residual 220.00 66.49 153.51 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA TYR M 236 " pdb=" C TYR M 236 " pdb=" N MET M 237 " pdb=" CA MET M 237 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR K 236 " pdb=" C TYR K 236 " pdb=" N MET K 237 " pdb=" CA MET K 237 " ideal model delta harmonic sigma weight residual 180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2095 0.051 - 0.102: 864 0.102 - 0.153: 205 0.153 - 0.204: 74 0.204 - 0.256: 9 Chirality restraints: 3247 Sorted by residual: chirality pdb=" CA ARG L 248 " pdb=" N ARG L 248 " pdb=" C ARG L 248 " pdb=" CB ARG L 248 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ARG N 248 " pdb=" N ARG N 248 " pdb=" C ARG N 248 " pdb=" CB ARG N 248 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3244 not shown) Planarity restraints: 2533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ALA G 52 " -0.077 2.00e-02 2.50e+03 pdb=" O ALA G 52 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA G 53 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C LYS F 59 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS F 59 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 60 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 32 " 0.038 2.00e-02 2.50e+03 1.74e-02 7.61e+00 pdb=" N1 DT I 32 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DT I 32 " -0.010 2.00e-02 2.50e+03 pdb=" O2 DT I 32 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DT I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 32 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT I 32 " 0.024 2.00e-02 2.50e+03 pdb=" C5 DT I 32 " -0.010 2.00e-02 2.50e+03 pdb=" C7 DT I 32 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 32 " -0.021 2.00e-02 2.50e+03 ... (remaining 2530 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 39 2.33 - 2.97: 8793 2.97 - 3.61: 30401 3.61 - 4.26: 51634 4.26 - 4.90: 76401 Nonbonded interactions: 167268 Sorted by model distance: nonbonded pdb=" NZ LYS C 75 " pdb=" P DA J 157 " model vdw 1.688 3.480 nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" NZ LYS C 75 " pdb=" OP1 DA J 157 " model vdw 1.752 3.120 nonbonded pdb=" NH2 ARG G 17 " pdb=" OP2 DA J 55 " model vdw 1.851 3.120 nonbonded pdb=" NH2 ARG F 36 " pdb=" OP1 DA J 85 " model vdw 1.906 3.120 ... (remaining 167263 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 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.180 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3686 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 : 0.007 0.074 20343 Z= 0.541 Angle : 1.036 8.665 28958 Z= 0.815 Chirality : 0.061 0.256 3247 Planarity : 0.005 0.045 2533 Dihedral : 25.641 153.511 8512 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.15 % Allowed : 2.82 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1530 helix: 0.79 (0.18), residues: 629 sheet: 0.45 (0.26), residues: 312 loop : 0.31 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 267 TYR 0.026 0.003 TYR B 88 PHE 0.018 0.002 PHE N 270 TRP 0.005 0.002 TRP N 146 HIS 0.010 0.002 HIS K 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.54 (20343) covalent geometry : angle 1.03596 / 0.81 (28958) hydrogen bonds : bond 0.11687 / 7.99 ( 1059) hydrogen bonds : angle 5.43389 / 3.98 ( 2621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8908 (mp0) cc_final: 0.8642 (mp0) REVERT: B 61 PHE cc_start: 0.8162 (t80) cc_final: 0.7950 (t80) REVERT: B 63 GLU cc_start: 0.8532 (pt0) cc_final: 0.8078 (pp20) REVERT: D 66 ILE cc_start: 0.9287 (mm) cc_final: 0.8980 (mm) REVERT: E 105 GLU cc_start: 0.8592 (tp30) cc_final: 0.8107 (tm-30) REVERT: G 25 PHE cc_start: 0.8614 (m-80) cc_final: 0.8034 (m-80) REVERT: G 54 VAL cc_start: 0.9539 (m) cc_final: 0.9224 (m) REVERT: K 243 MET cc_start: 0.3388 (ptp) cc_final: 0.2774 (ptt) REVERT: L 160 MET cc_start: 0.3291 (ttm) cc_final: 0.2313 (mtp) outliers start: 2 outliers final: 0 residues processed: 266 average time/residue: 0.1466 time to fit residues: 58.0617 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 3.9990 overall best weight: 4.9126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 81 ASN F 75 HIS G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 ASN L 288 ASN M 104 GLN M 178 HIS M 214 HIS M 235 ASN M 268 ASN M 288 ASN N 214 HIS N 268 ASN N 288 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.093090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.067068 restraints weight = 200403.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.067829 restraints weight = 112930.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.068173 restraints weight = 75243.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.068917 restraints weight = 55166.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.069008 restraints weight = 44300.783| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 20343 Z= 0.205 Angle : 0.758 8.234 28958 Z= 0.426 Chirality : 0.051 0.270 3247 Planarity : 0.006 0.056 2533 Dihedral : 29.810 160.174 5455 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.30 % Allowed : 2.75 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1530 helix: 1.43 (0.19), residues: 627 sheet: 0.56 (0.26), residues: 320 loop : 0.49 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.028 0.002 TYR L 205 PHE 0.028 0.003 PHE E 104 TRP 0.023 0.003 TRP N 146 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (20343) covalent geometry : angle 0.75775 / 0.43 (28958) hydrogen bonds : bond 0.06880 / 4.65 ( 1059) hydrogen bonds : angle 4.20221 / 3.13 ( 2621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8037 (tp30) cc_final: 0.7827 (tp30) REVERT: A 84 PHE cc_start: 0.8873 (m-10) cc_final: 0.8594 (m-10) REVERT: A 105 GLU cc_start: 0.9110 (tp30) cc_final: 0.8864 (tp30) REVERT: A 106 ASP cc_start: 0.8805 (m-30) cc_final: 0.8603 (m-30) REVERT: B 53 GLU cc_start: 0.9055 (mp0) cc_final: 0.8727 (mp0) REVERT: B 63 GLU cc_start: 0.8777 (pt0) cc_final: 0.8140 (pp20) REVERT: B 81 VAL cc_start: 0.8134 (m) cc_final: 0.7892 (m) REVERT: B 93 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 51 LEU cc_start: 0.9646 (tt) cc_final: 0.9386 (tt) REVERT: D 59 MET cc_start: 0.9155 (mmp) cc_final: 0.8668 (mmm) REVERT: D 65 ASP cc_start: 0.9237 (t0) cc_final: 0.9001 (t0) REVERT: E 105 GLU cc_start: 0.9077 (tp30) cc_final: 0.8387 (tm-30) REVERT: E 119 ILE cc_start: 0.8370 (pt) cc_final: 0.8141 (pt) REVERT: G 25 PHE cc_start: 0.8824 (m-10) cc_final: 0.8510 (m-80) REVERT: G 38 ASN cc_start: 0.6922 (OUTLIER) cc_final: 0.6353 (t0) REVERT: G 65 LEU cc_start: 0.9499 (tp) cc_final: 0.9246 (tp) REVERT: H 51 ILE cc_start: 0.8082 (tt) cc_final: 0.7056 (mp) REVERT: K 162 ILE cc_start: 0.3746 (pt) cc_final: 0.3384 (mm) REVERT: K 243 MET cc_start: 0.1806 (ptp) cc_final: 0.1553 (ptt) outliers start: 4 outliers final: 1 residues processed: 192 average time/residue: 0.1266 time to fit residues: 38.1161 Evaluate side-chains 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 140 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 134 optimal weight: 0.0970 chunk 164 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 chunk 167 optimal weight: 10.0000 overall best weight: 6.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 HIS L 239 ASN L 268 ASN M 100 GLN M 239 ASN N 193 HIS ** N 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.083933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.056452 restraints weight = 205049.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056570 restraints weight = 111879.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.056928 restraints weight = 73129.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.057197 restraints weight = 54552.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.057627 restraints weight = 45300.068| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 20343 Z= 0.239 Angle : 0.761 12.077 28958 Z= 0.432 Chirality : 0.050 0.334 3247 Planarity : 0.006 0.076 2533 Dihedral : 29.988 162.128 5455 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.45 % Allowed : 3.64 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1530 helix: 1.02 (0.19), residues: 627 sheet: 0.37 (0.28), residues: 324 loop : 0.21 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG L 196 TYR 0.044 0.003 TYR L 205 PHE 0.031 0.003 PHE L 113 TRP 0.008 0.002 TRP L 146 HIS 0.010 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (20343) covalent geometry : angle 0.76139 / 0.43 (28958) hydrogen bonds : bond 0.06751 / 4.46 ( 1059) hydrogen bonds : angle 4.35311 / 3.25 ( 2621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8501 (tp30) cc_final: 0.7847 (tp30) REVERT: A 84 PHE cc_start: 0.9059 (m-10) cc_final: 0.8592 (m-10) REVERT: A 105 GLU cc_start: 0.9130 (tp30) cc_final: 0.8713 (tm-30) REVERT: A 106 ASP cc_start: 0.8979 (m-30) cc_final: 0.8042 (m-30) REVERT: A 120 MET cc_start: 0.7547 (tpt) cc_final: 0.7247 (mmm) REVERT: B 46 ILE cc_start: 0.8863 (mp) cc_final: 0.8522 (mp) REVERT: B 53 GLU cc_start: 0.9151 (mp0) cc_final: 0.8887 (mp0) REVERT: B 63 GLU cc_start: 0.8965 (pt0) cc_final: 0.8466 (pp20) REVERT: D 59 MET cc_start: 0.9320 (mmp) cc_final: 0.9015 (mmm) REVERT: D 65 ASP cc_start: 0.9215 (t0) cc_final: 0.8988 (t0) REVERT: D 66 ILE cc_start: 0.9688 (mm) cc_final: 0.9472 (mm) REVERT: E 105 GLU cc_start: 0.9227 (tp30) cc_final: 0.8807 (tm-30) REVERT: F 63 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8565 (mt-10) REVERT: F 84 MET cc_start: 0.8712 (tpp) cc_final: 0.8314 (tpt) REVERT: G 65 LEU cc_start: 0.9636 (tp) cc_final: 0.9391 (tp) REVERT: K 246 MET cc_start: 0.5103 (mtm) cc_final: 0.4876 (mtt) outliers start: 6 outliers final: 2 residues processed: 167 average time/residue: 0.1219 time to fit residues: 32.1992 Evaluate side-chains 120 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 151 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 40.0000 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 84 optimal weight: 40.0000 chunk 139 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 24 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS K 239 ASN L 168 HIS N 100 GLN N 233 HIS N 239 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.082358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.053831 restraints weight = 203422.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.054554 restraints weight = 111493.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.054465 restraints weight = 71750.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.054620 restraints weight = 53348.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.054739 restraints weight = 44470.512| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20343 Z= 0.152 Angle : 0.641 8.919 28958 Z= 0.364 Chirality : 0.046 0.271 3247 Planarity : 0.004 0.032 2533 Dihedral : 29.931 166.911 5455 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1530 helix: 1.57 (0.20), residues: 627 sheet: 0.39 (0.28), residues: 324 loop : 0.20 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 196 TYR 0.023 0.002 TYR D 37 PHE 0.035 0.002 PHE K 212 TRP 0.009 0.001 TRP N 146 HIS 0.005 0.001 HIS N 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (20343) covalent geometry : angle 0.64107 / 0.36 (28958) hydrogen bonds : bond 0.05464 / 3.63 ( 1059) hydrogen bonds : angle 3.94741 / 2.94 ( 2621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8544 (tp30) cc_final: 0.7949 (tp30) REVERT: A 84 PHE cc_start: 0.9050 (m-10) cc_final: 0.8634 (m-10) REVERT: A 105 GLU cc_start: 0.9136 (tp30) cc_final: 0.8755 (tm-30) REVERT: A 106 ASP cc_start: 0.9018 (m-30) cc_final: 0.8046 (m-30) REVERT: A 120 MET cc_start: 0.7383 (tpt) cc_final: 0.6997 (mmm) REVERT: B 50 ILE cc_start: 0.9423 (pt) cc_final: 0.8879 (mm) REVERT: B 53 GLU cc_start: 0.9167 (mp0) cc_final: 0.8768 (mp0) REVERT: B 63 GLU cc_start: 0.9007 (pt0) cc_final: 0.8544 (pp20) REVERT: C 90 ASP cc_start: 0.7895 (t0) cc_final: 0.7490 (t70) REVERT: D 59 MET cc_start: 0.9404 (mmp) cc_final: 0.9147 (mmm) REVERT: D 65 ASP cc_start: 0.9295 (t0) cc_final: 0.9020 (t0) REVERT: E 67 PHE cc_start: 0.8895 (t80) cc_final: 0.8687 (t80) REVERT: E 105 GLU cc_start: 0.9321 (tp30) cc_final: 0.8908 (tm-30) REVERT: F 50 ILE cc_start: 0.9008 (mm) cc_final: 0.8801 (mm) REVERT: F 63 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8914 (mp0) REVERT: G 65 LEU cc_start: 0.9622 (tp) cc_final: 0.9368 (tp) REVERT: G 91 GLU cc_start: 0.9283 (pm20) cc_final: 0.9073 (pm20) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1170 time to fit residues: 28.2217 Evaluate side-chains 113 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 131 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 40.0000 chunk 101 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.068827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.039234 restraints weight = 172459.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.039418 restraints weight = 101940.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.039748 restraints weight = 71626.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040112 restraints weight = 56343.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040215 restraints weight = 49657.625| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 20343 Z= 0.216 Angle : 0.703 9.783 28958 Z= 0.400 Chirality : 0.047 0.239 3247 Planarity : 0.005 0.059 2533 Dihedral : 29.926 171.527 5455 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.07 % Allowed : 2.67 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1530 helix: 1.32 (0.20), residues: 627 sheet: 0.68 (0.28), residues: 316 loop : 0.16 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 40 TYR 0.023 0.002 TYR D 37 PHE 0.031 0.002 PHE A 67 TRP 0.009 0.001 TRP L 146 HIS 0.012 0.002 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.22 (20343) covalent geometry : angle 0.70283 / 0.40 (28958) hydrogen bonds : bond 0.08104 / 5.43 ( 1059) hydrogen bonds : angle 4.28210 / 3.17 ( 2621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8732 (tp30) cc_final: 0.8105 (tp30) REVERT: A 84 PHE cc_start: 0.9160 (m-10) cc_final: 0.8646 (m-10) REVERT: A 105 GLU cc_start: 0.9240 (tp30) cc_final: 0.8830 (tm-30) REVERT: A 106 ASP cc_start: 0.9183 (m-30) cc_final: 0.8287 (m-30) REVERT: B 50 ILE cc_start: 0.9374 (pt) cc_final: 0.8896 (mm) REVERT: B 53 GLU cc_start: 0.9314 (mp0) cc_final: 0.9027 (mp0) REVERT: B 63 GLU cc_start: 0.9173 (pt0) cc_final: 0.8683 (pp20) REVERT: B 68 ASP cc_start: 0.9189 (m-30) cc_final: 0.8979 (m-30) REVERT: E 105 GLU cc_start: 0.9345 (tp30) cc_final: 0.9040 (tm-30) REVERT: F 50 ILE cc_start: 0.8892 (mm) cc_final: 0.8529 (mm) REVERT: F 53 GLU cc_start: 0.9511 (mp0) cc_final: 0.9272 (pm20) REVERT: F 63 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8676 (mt-10) REVERT: F 84 MET cc_start: 0.8820 (tpp) cc_final: 0.8374 (tpp) REVERT: K 246 MET cc_start: 0.4323 (mtm) cc_final: 0.3804 (ptp) REVERT: L 205 TYR cc_start: -0.2040 (m-10) cc_final: -0.2542 (m-10) REVERT: M 246 MET cc_start: 0.7832 (pmm) cc_final: 0.7626 (pmm) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1208 time to fit residues: 24.4934 Evaluate side-chains 95 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 50.0000 chunk 179 optimal weight: 40.0000 chunk 168 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 40.0000 chunk 114 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 93 GLN L 193 HIS L 268 ASN M 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.069017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039182 restraints weight = 172067.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.039034 restraints weight = 101382.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.039461 restraints weight = 72326.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.039790 restraints weight = 57887.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.039917 restraints weight = 50522.504| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20343 Z= 0.142 Angle : 0.595 8.986 28958 Z= 0.340 Chirality : 0.044 0.298 3247 Planarity : 0.004 0.068 2533 Dihedral : 29.988 173.424 5455 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1530 helix: 1.62 (0.20), residues: 627 sheet: 0.79 (0.30), residues: 288 loop : 0.14 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG K 196 TYR 0.014 0.001 TYR C 57 PHE 0.011 0.001 PHE N 212 TRP 0.010 0.001 TRP L 146 HIS 0.006 0.001 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (20343) covalent geometry : angle 0.59471 / 0.34 (28958) hydrogen bonds : bond 0.05187 / 3.45 ( 1059) hydrogen bonds : angle 3.92403 / 2.92 ( 2621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8603 (tp30) cc_final: 0.7907 (tp30) REVERT: A 84 PHE cc_start: 0.9145 (m-10) cc_final: 0.8726 (m-10) REVERT: A 105 GLU cc_start: 0.9276 (tp30) cc_final: 0.8924 (tm-30) REVERT: A 120 MET cc_start: 0.8017 (tpt) cc_final: 0.7607 (mmm) REVERT: B 50 ILE cc_start: 0.9231 (pt) cc_final: 0.8975 (pt) REVERT: B 53 GLU cc_start: 0.9244 (mp0) cc_final: 0.8971 (mp0) REVERT: B 63 GLU cc_start: 0.9160 (pt0) cc_final: 0.8649 (pp20) REVERT: B 68 ASP cc_start: 0.9148 (m-30) cc_final: 0.8908 (m-30) REVERT: D 65 ASP cc_start: 0.9397 (t0) cc_final: 0.9176 (t0) REVERT: E 106 ASP cc_start: 0.9019 (m-30) cc_final: 0.8428 (p0) REVERT: F 50 ILE cc_start: 0.8920 (mm) cc_final: 0.8625 (mm) REVERT: F 84 MET cc_start: 0.8635 (tpp) cc_final: 0.8178 (tpt) REVERT: K 202 ARG cc_start: 0.5877 (tmt170) cc_final: 0.5662 (tpt90) REVERT: K 246 MET cc_start: 0.3923 (mtm) cc_final: 0.3440 (ptp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1282 time to fit residues: 25.9979 Evaluate side-chains 92 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 161 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 40.0000 chunk 37 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 162 optimal weight: 50.0000 chunk 53 optimal weight: 0.1980 chunk 167 optimal weight: 8.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.067466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037460 restraints weight = 172822.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037548 restraints weight = 101513.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.037883 restraints weight = 71781.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038166 restraints weight = 56609.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038253 restraints weight = 49034.244| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20343 Z= 0.155 Angle : 0.592 10.570 28958 Z= 0.342 Chirality : 0.043 0.286 3247 Planarity : 0.004 0.037 2533 Dihedral : 29.851 175.438 5455 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.21), residues: 1530 helix: 1.69 (0.20), residues: 630 sheet: 0.69 (0.29), residues: 316 loop : 0.17 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 290 TYR 0.021 0.001 TYR D 34 PHE 0.028 0.001 PHE A 67 TRP 0.009 0.001 TRP L 146 HIS 0.016 0.002 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (20343) covalent geometry : angle 0.59198 / 0.34 (28958) hydrogen bonds : bond 0.05656 / 3.78 ( 1059) hydrogen bonds : angle 3.93423 / 2.93 ( 2621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8651 (tp30) cc_final: 0.8043 (tp30) REVERT: A 84 PHE cc_start: 0.9042 (m-10) cc_final: 0.8695 (m-10) REVERT: A 105 GLU cc_start: 0.9371 (tp30) cc_final: 0.8934 (tm-30) REVERT: A 120 MET cc_start: 0.8227 (tpt) cc_final: 0.7735 (mmm) REVERT: B 50 ILE cc_start: 0.9289 (pt) cc_final: 0.9064 (pt) REVERT: B 53 GLU cc_start: 0.9263 (mp0) cc_final: 0.8999 (mp0) REVERT: B 63 GLU cc_start: 0.9181 (pt0) cc_final: 0.8673 (pp20) REVERT: B 68 ASP cc_start: 0.9144 (m-30) cc_final: 0.8880 (m-30) REVERT: D 65 ASP cc_start: 0.9395 (t0) cc_final: 0.9192 (t0) REVERT: E 77 ASP cc_start: 0.9306 (m-30) cc_final: 0.9101 (m-30) REVERT: E 90 MET cc_start: 0.9590 (mmp) cc_final: 0.9327 (mmm) REVERT: E 97 GLU cc_start: 0.8679 (pp20) cc_final: 0.8462 (pp20) REVERT: E 105 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8711 (tm-30) REVERT: F 50 ILE cc_start: 0.8873 (mm) cc_final: 0.8608 (mm) REVERT: K 246 MET cc_start: 0.4587 (mtm) cc_final: 0.4027 (ptp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1272 time to fit residues: 24.3474 Evaluate side-chains 91 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 122 optimal weight: 40.0000 chunk 157 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 154 optimal weight: 40.0000 chunk 166 optimal weight: 40.0000 chunk 139 optimal weight: 0.7980 chunk 89 optimal weight: 50.0000 chunk 168 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 164 optimal weight: 30.0000 chunk 125 optimal weight: 0.0030 overall best weight: 6.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN K 100 GLN M 104 GLN N 233 HIS N 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.071903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041740 restraints weight = 210582.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041963 restraints weight = 113891.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042704 restraints weight = 71896.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.042126 restraints weight = 56690.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042163 restraints weight = 49730.425| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.8744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 20343 Z= 0.195 Angle : 0.667 10.460 28958 Z= 0.376 Chirality : 0.045 0.307 3247 Planarity : 0.005 0.075 2533 Dihedral : 30.025 178.979 5455 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.07 % Allowed : 1.34 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.21), residues: 1530 helix: 1.46 (0.20), residues: 630 sheet: 0.71 (0.30), residues: 288 loop : 0.04 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 290 TYR 0.062 0.002 TYR H 80 PHE 0.017 0.002 PHE E 67 TRP 0.008 0.001 TRP L 146 HIS 0.012 0.002 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (20343) covalent geometry : angle 0.66748 / 0.38 (28958) hydrogen bonds : bond 0.06773 / 4.59 ( 1059) hydrogen bonds : angle 4.17650 / 3.12 ( 2621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8695 (tp30) cc_final: 0.8060 (tp30) REVERT: A 84 PHE cc_start: 0.9077 (m-10) cc_final: 0.8723 (m-10) REVERT: A 105 GLU cc_start: 0.9400 (tp30) cc_final: 0.9088 (tm-30) REVERT: A 120 MET cc_start: 0.8607 (tpt) cc_final: 0.8216 (mmm) REVERT: B 50 ILE cc_start: 0.9310 (pt) cc_final: 0.9103 (pt) REVERT: B 53 GLU cc_start: 0.9351 (mp0) cc_final: 0.9100 (mp0) REVERT: B 63 GLU cc_start: 0.9308 (pt0) cc_final: 0.8753 (pp20) REVERT: B 68 ASP cc_start: 0.9194 (m-30) cc_final: 0.8973 (m-30) REVERT: E 90 MET cc_start: 0.9594 (mmp) cc_final: 0.9286 (mmm) REVERT: E 106 ASP cc_start: 0.9161 (m-30) cc_final: 0.8566 (p0) REVERT: F 50 ILE cc_start: 0.8789 (mm) cc_final: 0.8478 (mm) REVERT: F 53 GLU cc_start: 0.9579 (mp0) cc_final: 0.9325 (pm20) REVERT: F 84 MET cc_start: 0.9073 (tpp) cc_final: 0.8651 (tpp) REVERT: H 56 MET cc_start: 0.9364 (mmp) cc_final: 0.8959 (tpt) REVERT: K 246 MET cc_start: 0.4641 (mtm) cc_final: 0.4148 (mtm) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1324 time to fit residues: 23.2001 Evaluate side-chains 80 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 1 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS M 104 GLN ** N 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.071771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041683 restraints weight = 208227.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042059 restraints weight = 111515.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042558 restraints weight = 69881.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042633 restraints weight = 56882.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042578 restraints weight = 50408.329| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.9073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20343 Z= 0.153 Angle : 0.597 13.000 28958 Z= 0.341 Chirality : 0.043 0.292 3247 Planarity : 0.004 0.047 2533 Dihedral : 29.964 178.638 5455 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1530 helix: 1.66 (0.20), residues: 630 sheet: 0.71 (0.30), residues: 288 loop : 0.05 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.018 0.002 TYR H 80 PHE 0.014 0.001 PHE E 67 TRP 0.004 0.001 TRP K 146 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (20343) covalent geometry : angle 0.59713 / 0.34 (28958) hydrogen bonds : bond 0.05424 / 3.64 ( 1059) hydrogen bonds : angle 3.98270 / 2.97 ( 2621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8667 (tp30) cc_final: 0.8072 (tp30) REVERT: A 84 PHE cc_start: 0.9113 (m-10) cc_final: 0.8731 (m-10) REVERT: A 105 GLU cc_start: 0.9387 (tp30) cc_final: 0.9112 (tm-30) REVERT: A 120 MET cc_start: 0.8551 (tpt) cc_final: 0.8206 (mmm) REVERT: B 50 ILE cc_start: 0.9346 (pt) cc_final: 0.9145 (pt) REVERT: B 53 GLU cc_start: 0.9361 (mp0) cc_final: 0.9118 (mp0) REVERT: B 63 GLU cc_start: 0.9331 (pt0) cc_final: 0.8815 (pp20) REVERT: B 68 ASP cc_start: 0.9280 (m-30) cc_final: 0.9022 (m-30) REVERT: E 90 MET cc_start: 0.9611 (mmp) cc_final: 0.9260 (mmm) REVERT: E 106 ASP cc_start: 0.9164 (m-30) cc_final: 0.8581 (p0) REVERT: F 50 ILE cc_start: 0.8816 (mm) cc_final: 0.8442 (mm) REVERT: F 53 GLU cc_start: 0.9510 (mp0) cc_final: 0.9290 (pm20) REVERT: F 84 MET cc_start: 0.8680 (tpp) cc_final: 0.8459 (tpp) REVERT: K 246 MET cc_start: 0.4680 (mtm) cc_final: 0.4075 (mtm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1302 time to fit residues: 22.5905 Evaluate side-chains 81 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 50.0000 chunk 103 optimal weight: 50.0000 chunk 137 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 50.0000 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 84 optimal weight: 50.0000 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 104 GLN N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.064770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033520 restraints weight = 177692.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033754 restraints weight = 104129.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033917 restraints weight = 72543.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.034234 restraints weight = 57741.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034399 restraints weight = 50666.639| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.9260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20343 Z= 0.138 Angle : 0.590 14.924 28958 Z= 0.336 Chirality : 0.043 0.296 3247 Planarity : 0.004 0.037 2533 Dihedral : 29.886 178.734 5455 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1530 helix: 1.73 (0.20), residues: 630 sheet: 0.71 (0.30), residues: 288 loop : 0.01 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 29 TYR 0.016 0.001 TYR F 51 PHE 0.015 0.001 PHE G 25 TRP 0.004 0.001 TRP K 146 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (20343) covalent geometry : angle 0.58986 / 0.34 (28958) hydrogen bonds : bond 0.05184 / 3.47 ( 1059) hydrogen bonds : angle 3.89167 / 2.89 ( 2621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8590 (tp30) cc_final: 0.8022 (tp30) REVERT: A 84 PHE cc_start: 0.9158 (m-10) cc_final: 0.8743 (m-10) REVERT: A 105 GLU cc_start: 0.9351 (tp30) cc_final: 0.9089 (tm-30) REVERT: A 120 MET cc_start: 0.8553 (tpt) cc_final: 0.8220 (mmm) REVERT: B 53 GLU cc_start: 0.9311 (mp0) cc_final: 0.9107 (mp0) REVERT: B 63 GLU cc_start: 0.9330 (pt0) cc_final: 0.8833 (pp20) REVERT: B 68 ASP cc_start: 0.9221 (m-30) cc_final: 0.8960 (m-30) REVERT: E 77 ASP cc_start: 0.9421 (m-30) cc_final: 0.8669 (m-30) REVERT: E 90 MET cc_start: 0.9584 (mmp) cc_final: 0.9253 (mmm) REVERT: E 106 ASP cc_start: 0.9090 (m-30) cc_final: 0.8559 (p0) REVERT: F 50 ILE cc_start: 0.8827 (mm) cc_final: 0.8532 (mm) REVERT: F 84 MET cc_start: 0.8610 (tpp) cc_final: 0.8358 (tpp) REVERT: K 246 MET cc_start: 0.4813 (mtm) cc_final: 0.4100 (mtm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1228 time to fit residues: 20.9880 Evaluate side-chains 84 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 123 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 11 optimal weight: 0.0060 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 167 optimal weight: 50.0000 chunk 151 optimal weight: 50.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 104 GLN N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.064564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033589 restraints weight = 178545.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.033390 restraints weight = 104055.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.033541 restraints weight = 72623.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033778 restraints weight = 59390.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.033860 restraints weight = 51759.478| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.9461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20343 Z= 0.138 Angle : 0.579 13.879 28958 Z= 0.331 Chirality : 0.042 0.286 3247 Planarity : 0.004 0.037 2533 Dihedral : 29.812 178.429 5455 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.21), residues: 1530 helix: 1.81 (0.20), residues: 630 sheet: 0.73 (0.30), residues: 288 loop : -0.01 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 175 TYR 0.014 0.001 TYR G 50 PHE 0.014 0.001 PHE G 25 TRP 0.004 0.001 TRP K 146 HIS 0.005 0.001 HIS N 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (20343) covalent geometry : angle 0.57855 / 0.33 (28958) hydrogen bonds : bond 0.05107 / 3.43 ( 1059) hydrogen bonds : angle 3.85199 / 2.86 ( 2621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.65 seconds wall clock time: 86 minutes 33.38 seconds (5193.38 seconds total)