Starting phenix.real_space_refine on Sat Sep 12 21:54:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzx_33533/09_2026/7xzx_33533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzx_33533/09_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_33533/09_2026/7xzx_33533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzx_33533/09_2026/7xzx_33533.map" model { file = "/net/cci-nas-00/data/ceres_data/7xzx_33533/09_2026/7xzx_33533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzx_33533/09_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-2.2.1-6174/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: 3.62, per 1000 atoms: 0.19 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: 1.53 Conformation dependent library (CDL) restraints added in 542.2 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: 2.12 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: 3.76 Time building geometry restraints manager: 2.05 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: 26264 1.73 - 3.47: 2368 3.47 - 5.20: 254 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.570 Find NCS groups from input model: 0.280 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- 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= 0.544 Angle : 1.040 8.665 28958 Z= 0.819 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 1.04027 / 0.82 (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 : 0.637 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: symmetry clash REVERT: B 53 GLU cc_start: 0.8908 (mp0) cc_final: 0.8641 (mp0) REVERT: B 61 PHE cc_start: 0.8162 (t80) cc_final: 0.7952 (t80) REVERT: B 63 GLU cc_start: 0.8532 (pt0) cc_final: 0.8077 (pp20) REVERT: D 66 ILE cc_start: 0.9287 (mm) cc_final: 0.8981 (mm) REVERT: E 105 GLU cc_start: 0.8592 (tp30) cc_final: 0.8101 (tm-30) REVERT: G 25 PHE cc_start: 0.8614 (m-80) cc_final: 0.8032 (m-80) REVERT: G 38 ASN cc_start: 0.7684 (m-40) cc_final: 0.7482 (t0) REVERT: G 54 VAL cc_start: 0.9539 (m) cc_final: 0.9225 (m) REVERT: K 243 MET cc_start: 0.3388 (ptp) cc_final: 0.2773 (ptt) REVERT: L 160 MET cc_start: 0.3291 (ttm) cc_final: 0.2312 (mtp) outliers start: 2 outliers final: 0 residues processed: 266 average time/residue: 0.1510 time to fit residues: 60.2031 Evaluate side-chains 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 overall best weight: 4.3124 ------------------------------------------------------------------------------- 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 ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 ASN L 288 ASN ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.094111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.068087 restraints weight = 201468.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.068462 restraints weight = 113722.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.069052 restraints weight = 76939.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.069364 restraints weight = 57027.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.070068 restraints weight = 47116.824| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 20343 Z= 0.193 Angle : 0.752 7.610 28958 Z= 0.421 Chirality : 0.051 0.289 3247 Planarity : 0.005 0.055 2533 Dihedral : 29.710 159.091 5455 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.22 % Allowed : 2.82 % 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: 1.28 (0.20), residues: 1530 helix: 1.46 (0.19), residues: 627 sheet: 0.54 (0.26), residues: 320 loop : 0.53 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 202 TYR 0.025 0.002 TYR L 205 PHE 0.027 0.003 PHE E 104 TRP 0.021 0.003 TRP N 146 HIS 0.007 0.001 HIS N 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (20343) covalent geometry : angle 0.75244 / 0.42 (28958) hydrogen bonds : bond 0.06546 / 4.40 ( 1059) hydrogen bonds : angle 4.18206 / 3.12 ( 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 195 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.532 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: A 73 GLU cc_start: 0.7895 (tp30) cc_final: 0.7677 (tp30) REVERT: A 84 PHE cc_start: 0.8817 (m-10) cc_final: 0.8552 (m-10) REVERT: A 105 GLU cc_start: 0.9090 (tp30) cc_final: 0.8854 (tp30) REVERT: A 120 MET cc_start: 0.5793 (mmp) cc_final: 0.5573 (mmm) REVERT: B 53 GLU cc_start: 0.9043 (mp0) cc_final: 0.8699 (mp0) REVERT: B 63 GLU cc_start: 0.8760 (pt0) cc_final: 0.8181 (pp20) REVERT: B 81 VAL cc_start: 0.8007 (m) cc_final: 0.7744 (m) REVERT: B 98 TYR cc_start: 0.8589 (m-10) cc_final: 0.8309 (m-80) REVERT: C 39 TYR cc_start: 0.8743 (m-80) cc_final: 0.8163 (m-80) REVERT: C 51 LEU cc_start: 0.9635 (tt) cc_final: 0.9359 (tt) REVERT: D 59 MET cc_start: 0.9080 (mmp) cc_final: 0.8609 (mmm) REVERT: D 65 ASP cc_start: 0.9224 (t0) cc_final: 0.8980 (t0) REVERT: E 105 GLU cc_start: 0.9058 (tp30) cc_final: 0.8378 (tm-30) REVERT: E 119 ILE cc_start: 0.8329 (pt) cc_final: 0.8078 (pt) REVERT: G 25 PHE cc_start: 0.8727 (m-10) cc_final: 0.8336 (m-80) REVERT: G 65 LEU cc_start: 0.9478 (tp) cc_final: 0.9212 (tp) REVERT: H 51 ILE cc_start: 0.8060 (tt) cc_final: 0.7035 (mp) REVERT: K 162 ILE cc_start: 0.3810 (pt) cc_final: 0.3424 (mm) REVERT: K 243 MET cc_start: 0.1798 (ptp) cc_final: 0.1544 (ptt) outliers start: 3 outliers final: 1 residues processed: 195 average time/residue: 0.1314 time to fit residues: 40.2244 Evaluate side-chains 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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: 50.0000 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 179 optimal weight: 30.0000 chunk 117 optimal weight: 50.0000 chunk 121 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 chunk 164 optimal weight: 50.0000 chunk 27 optimal weight: 20.0000 chunk 147 optimal weight: 50.0000 chunk 167 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 75 HIS ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN L 214 HIS L 239 ASN L 268 ASN M 100 GLN M 104 GLN M 193 HIS M 239 ASN N 193 HIS ** N 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.084592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.056849 restraints weight = 204650.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.057479 restraints weight = 113108.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.057895 restraints weight = 73341.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.058294 restraints weight = 54863.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.058384 restraints weight = 45307.787| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 20343 Z= 0.241 Angle : 0.760 10.998 28958 Z= 0.428 Chirality : 0.050 0.235 3247 Planarity : 0.006 0.072 2533 Dihedral : 29.858 160.249 5455 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.22 % Allowed : 3.79 % Favored : 95.99 % 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: 1.09 (0.19), residues: 625 sheet: 0.34 (0.28), residues: 324 loop : 0.15 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 196 TYR 0.043 0.003 TYR C 57 PHE 0.033 0.003 PHE L 113 TRP 0.008 0.002 TRP L 146 HIS 0.008 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 (20343) covalent geometry : angle 0.75953 / 0.43 (28958) hydrogen bonds : bond 0.07020 / 4.68 ( 1059) hydrogen bonds : angle 4.28564 / 3.21 ( 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 167 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.602 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: 0.8500 (tp30) cc_final: 0.7830 (tp30) REVERT: A 84 PHE cc_start: 0.9148 (m-10) cc_final: 0.8686 (m-10) REVERT: A 105 GLU cc_start: 0.9117 (tp30) cc_final: 0.8701 (tm-30) REVERT: A 106 ASP cc_start: 0.8945 (m-30) cc_final: 0.8009 (m-30) REVERT: B 53 GLU cc_start: 0.9224 (mp0) cc_final: 0.8940 (mp0) REVERT: B 63 GLU cc_start: 0.8980 (pt0) cc_final: 0.8476 (pp20) REVERT: D 59 MET cc_start: 0.9348 (mmp) cc_final: 0.9007 (mmm) REVERT: E 105 GLU cc_start: 0.9242 (tp30) cc_final: 0.8777 (tm-30) REVERT: F 50 ILE cc_start: 0.9064 (mm) cc_final: 0.8858 (mm) REVERT: F 84 MET cc_start: 0.8733 (tpp) cc_final: 0.8328 (tpt) REVERT: G 25 PHE cc_start: 0.9154 (m-80) cc_final: 0.8817 (m-10) REVERT: G 65 LEU cc_start: 0.9660 (tp) cc_final: 0.9416 (tp) REVERT: G 91 GLU cc_start: 0.9192 (pm20) cc_final: 0.8922 (pm20) REVERT: H 32 GLU cc_start: 0.8045 (tp30) cc_final: 0.7839 (mp0) REVERT: K 243 MET cc_start: 0.2599 (ptp) cc_final: 0.2387 (ptt) outliers start: 3 outliers final: 0 residues processed: 165 average time/residue: 0.1312 time to fit residues: 34.3137 Evaluate side-chains 118 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 139 optimal weight: 30.0000 chunk 95 optimal weight: 50.0000 chunk 15 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN H 46 HIS L 268 ASN N 100 GLN N 233 HIS N 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.080446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.051829 restraints weight = 203883.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.051884 restraints weight = 111765.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052306 restraints weight = 74511.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.052631 restraints weight = 55842.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.052754 restraints weight = 47268.114| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20343 Z= 0.204 Angle : 0.718 9.581 28958 Z= 0.398 Chirality : 0.047 0.299 3247 Planarity : 0.005 0.074 2533 Dihedral : 29.934 166.421 5455 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 0.99 (0.21), residues: 1530 helix: 1.37 (0.20), residues: 626 sheet: 0.41 (0.27), residues: 328 loop : 0.17 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 196 TYR 0.017 0.002 TYR C 57 PHE 0.028 0.002 PHE N 212 TRP 0.011 0.002 TRP N 146 HIS 0.007 0.001 HIS M 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (20343) covalent geometry : angle 0.71831 / 0.40 (28958) hydrogen bonds : bond 0.06375 / 4.24 ( 1059) hydrogen bonds : angle 4.07873 / 3.03 ( 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 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8635 (tp30) cc_final: 0.8029 (tp30) REVERT: A 84 PHE cc_start: 0.9005 (m-10) cc_final: 0.8531 (m-10) REVERT: A 105 GLU cc_start: 0.9151 (tp30) cc_final: 0.8796 (tm-30) REVERT: A 106 ASP cc_start: 0.9107 (m-30) cc_final: 0.8134 (m-30) REVERT: B 53 GLU cc_start: 0.9264 (mp0) cc_final: 0.8954 (mp0) REVERT: B 63 GLU cc_start: 0.9008 (pt0) cc_final: 0.8429 (pp20) REVERT: D 59 MET cc_start: 0.9515 (mmp) cc_final: 0.9287 (mmm) REVERT: E 97 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8809 (tm-30) REVERT: E 105 GLU cc_start: 0.9330 (tp30) cc_final: 0.9044 (tm-30) REVERT: E 106 ASP cc_start: 0.9070 (m-30) cc_final: 0.8661 (m-30) REVERT: E 119 ILE cc_start: 0.8697 (pt) cc_final: 0.8450 (pt) REVERT: F 50 ILE cc_start: 0.8888 (mm) cc_final: 0.8366 (mm) REVERT: F 53 GLU cc_start: 0.9542 (mp0) cc_final: 0.9257 (pm20) REVERT: F 63 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8963 (mp0) REVERT: F 84 MET cc_start: 0.8679 (tpp) cc_final: 0.8331 (tpt) REVERT: G 65 LEU cc_start: 0.9630 (tp) cc_final: 0.9373 (tp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1251 time to fit residues: 29.0065 Evaluate side-chains 105 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 50.0000 chunk 163 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 40.0000 chunk 101 optimal weight: 40.0000 chunk 51 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 50.0000 chunk 112 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 24 GLN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.071883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042550 restraints weight = 169318.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.042833 restraints weight = 99164.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.043255 restraints weight = 68559.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.043593 restraints weight = 53452.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.043695 restraints weight = 45835.264| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20343 Z= 0.151 Angle : 0.620 8.540 28958 Z= 0.352 Chirality : 0.045 0.260 3247 Planarity : 0.004 0.037 2533 Dihedral : 29.815 167.187 5455 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 1.18 (0.21), residues: 1530 helix: 1.62 (0.20), residues: 625 sheet: 0.38 (0.28), residues: 324 loop : 0.25 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 181 TYR 0.022 0.002 TYR L 205 PHE 0.044 0.002 PHE A 67 TRP 0.008 0.001 TRP L 146 HIS 0.009 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (20343) covalent geometry : angle 0.61972 / 0.35 (28958) hydrogen bonds : bond 0.05372 / 3.58 ( 1059) hydrogen bonds : angle 3.94264 / 2.94 ( 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 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.687 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: 0.8584 (tp30) cc_final: 0.7901 (tp30) REVERT: A 84 PHE cc_start: 0.9042 (m-10) cc_final: 0.8538 (m-10) REVERT: A 105 GLU cc_start: 0.9268 (tp30) cc_final: 0.8839 (tm-30) REVERT: A 106 ASP cc_start: 0.9105 (m-30) cc_final: 0.8208 (m-30) REVERT: B 53 GLU cc_start: 0.9264 (mp0) cc_final: 0.8770 (pm20) REVERT: B 63 GLU cc_start: 0.9112 (pt0) cc_final: 0.8593 (pp20) REVERT: D 59 MET cc_start: 0.9539 (mmp) cc_final: 0.9331 (mmm) REVERT: E 105 GLU cc_start: 0.9303 (tp30) cc_final: 0.9017 (tm-30) REVERT: E 110 CYS cc_start: 0.9469 (t) cc_final: 0.9190 (p) REVERT: F 50 ILE cc_start: 0.8841 (mm) cc_final: 0.8593 (mm) REVERT: F 63 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8859 (mt-10) REVERT: G 65 LEU cc_start: 0.9582 (tp) cc_final: 0.9317 (tp) REVERT: K 243 MET cc_start: 0.1735 (ptt) cc_final: 0.1521 (ptt) REVERT: L 169 MET cc_start: 0.3475 (tpt) cc_final: 0.3269 (tpt) REVERT: L 205 TYR cc_start: -0.1702 (m-10) cc_final: -0.2192 (m-10) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1181 time to fit residues: 26.0545 Evaluate side-chains 102 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 9.9990 chunk 168 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS N 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.069138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038899 restraints weight = 172525.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.039438 restraints weight = 101845.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039778 restraints weight = 71616.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.039999 restraints weight = 56796.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040187 restraints weight = 49517.519| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20343 Z= 0.170 Angle : 0.634 9.406 28958 Z= 0.359 Chirality : 0.044 0.319 3247 Planarity : 0.005 0.065 2533 Dihedral : 29.755 170.343 5455 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.21), residues: 1530 helix: 1.63 (0.20), residues: 630 sheet: 0.60 (0.30), residues: 300 loop : 0.16 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 72 TYR 0.028 0.002 TYR C 57 PHE 0.013 0.001 PHE A 104 TRP 0.013 0.001 TRP L 146 HIS 0.029 0.002 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (20343) covalent geometry : angle 0.63373 / 0.36 (28958) hydrogen bonds : bond 0.06131 / 4.10 ( 1059) hydrogen bonds : angle 3.96132 / 2.96 ( 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 134 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8628 (tp30) cc_final: 0.7957 (tp30) REVERT: A 84 PHE cc_start: 0.9079 (m-10) cc_final: 0.8592 (m-10) REVERT: A 105 GLU cc_start: 0.9245 (tp30) cc_final: 0.8872 (tm-30) REVERT: A 106 ASP cc_start: 0.9161 (m-30) cc_final: 0.8293 (m-30) REVERT: B 53 GLU cc_start: 0.9337 (mp0) cc_final: 0.8854 (pm20) REVERT: B 63 GLU cc_start: 0.9174 (pt0) cc_final: 0.8685 (pp20) REVERT: B 68 ASP cc_start: 0.9189 (m-30) cc_final: 0.8966 (m-30) REVERT: E 77 ASP cc_start: 0.9246 (m-30) cc_final: 0.8996 (m-30) REVERT: E 90 MET cc_start: 0.9422 (mmm) cc_final: 0.9175 (mmm) REVERT: E 97 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8745 (mt-10) REVERT: E 106 ASP cc_start: 0.8993 (m-30) cc_final: 0.8371 (p0) REVERT: E 110 CYS cc_start: 0.9525 (t) cc_final: 0.9231 (p) REVERT: F 50 ILE cc_start: 0.8915 (mm) cc_final: 0.8336 (mm) REVERT: F 53 GLU cc_start: 0.9544 (mp0) cc_final: 0.9203 (pm20) REVERT: F 84 MET cc_start: 0.8769 (tpp) cc_final: 0.8425 (tpp) REVERT: G 65 LEU cc_start: 0.9582 (tp) cc_final: 0.9326 (tp) REVERT: K 202 ARG cc_start: 0.5854 (tmt170) cc_final: 0.5654 (tpt90) REVERT: L 169 MET cc_start: 0.4130 (tpt) cc_final: 0.3922 (tpt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1362 time to fit residues: 29.0932 Evaluate side-chains 93 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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: 40.0000 chunk 8 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 40.0000 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 162 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 113 HIS L 268 ASN ** M 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.068991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.038569 restraints weight = 171694.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.038876 restraints weight = 100961.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039222 restraints weight = 70736.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.039508 restraints weight = 55502.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.039600 restraints weight = 47958.930| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20343 Z= 0.139 Angle : 0.593 8.264 28958 Z= 0.338 Chirality : 0.043 0.306 3247 Planarity : 0.004 0.039 2533 Dihedral : 29.759 173.032 5455 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 1.40 (0.21), residues: 1530 helix: 1.84 (0.20), residues: 630 sheet: 0.65 (0.28), residues: 316 loop : 0.18 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 290 TYR 0.021 0.001 TYR M 163 PHE 0.021 0.001 PHE A 67 TRP 0.008 0.001 TRP L 146 HIS 0.015 0.001 HIS L 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (20343) covalent geometry : angle 0.59333 / 0.34 (28958) hydrogen bonds : bond 0.04988 / 3.29 ( 1059) hydrogen bonds : angle 3.85479 / 2.88 ( 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 124 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.577 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: 0.8594 (tp30) cc_final: 0.7953 (tp30) REVERT: A 84 PHE cc_start: 0.8979 (m-10) cc_final: 0.8558 (m-10) REVERT: A 105 GLU cc_start: 0.9291 (tp30) cc_final: 0.8957 (tm-30) REVERT: A 106 ASP cc_start: 0.9178 (m-30) cc_final: 0.8307 (m-30) REVERT: B 53 GLU cc_start: 0.9333 (mp0) cc_final: 0.8852 (pm20) REVERT: B 63 GLU cc_start: 0.9162 (pt0) cc_final: 0.8655 (pp20) REVERT: B 68 ASP cc_start: 0.9143 (m-30) cc_final: 0.8871 (m-30) REVERT: D 59 MET cc_start: 0.9594 (mmp) cc_final: 0.9364 (mmm) REVERT: E 77 ASP cc_start: 0.9496 (m-30) cc_final: 0.9257 (m-30) REVERT: E 110 CYS cc_start: 0.9519 (t) cc_final: 0.9215 (p) REVERT: F 50 ILE cc_start: 0.8861 (mm) cc_final: 0.8546 (mm) REVERT: F 63 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8879 (mt-10) REVERT: F 84 MET cc_start: 0.8723 (tpp) cc_final: 0.8366 (tpp) REVERT: K 202 ARG cc_start: 0.5964 (tmt170) cc_final: 0.5763 (tmt170) REVERT: K 246 MET cc_start: 0.4813 (mtm) cc_final: 0.4472 (mtm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1310 time to fit residues: 26.0920 Evaluate side-chains 94 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 50.0000 chunk 157 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 154 optimal weight: 50.0000 chunk 166 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 chunk 168 optimal weight: 50.0000 chunk 56 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN K 100 GLN L 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.062994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032599 restraints weight = 184127.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.033016 restraints weight = 110435.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033178 restraints weight = 78501.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.033458 restraints weight = 65256.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033549 restraints weight = 57015.018| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.9058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 20343 Z= 0.292 Angle : 0.829 15.007 28958 Z= 0.459 Chirality : 0.049 0.325 3247 Planarity : 0.006 0.052 2533 Dihedral : 30.028 175.743 5455 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 0.55 (0.21), residues: 1530 helix: 0.88 (0.19), residues: 630 sheet: 0.48 (0.30), residues: 288 loop : -0.08 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG K 196 TYR 0.034 0.003 TYR K 236 PHE 0.025 0.003 PHE E 67 TRP 0.012 0.001 TRP L 146 HIS 0.009 0.002 HIS K 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.29 (20343) covalent geometry : angle 0.82919 / 0.46 (28958) hydrogen bonds : bond 0.11083 / 7.54 ( 1059) hydrogen bonds : angle 4.70487 / 3.50 ( 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 103 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.535 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 84 PHE cc_start: 0.9328 (m-10) cc_final: 0.8845 (m-10) REVERT: A 105 GLU cc_start: 0.9408 (tp30) cc_final: 0.9042 (tm-30) REVERT: A 106 ASP cc_start: 0.9321 (m-30) cc_final: 0.8602 (m-30) REVERT: A 120 MET cc_start: 0.8175 (mmm) cc_final: 0.7727 (mmm) REVERT: B 53 GLU cc_start: 0.9498 (mp0) cc_final: 0.9140 (pm20) REVERT: B 63 GLU cc_start: 0.9332 (pt0) cc_final: 0.8799 (pp20) REVERT: E 90 MET cc_start: 0.9383 (mmm) cc_final: 0.9168 (mmm) REVERT: E 97 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8743 (mt-10) REVERT: F 84 MET cc_start: 0.8978 (tpp) cc_final: 0.8693 (tpp) REVERT: H 56 MET cc_start: 0.9418 (mmp) cc_final: 0.9100 (tpp) REVERT: K 246 MET cc_start: 0.4666 (mtm) cc_final: 0.4270 (ptp) REVERT: M 290 ARG cc_start: 0.7992 (tpp-160) cc_final: 0.7772 (mpt180) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1352 time to fit residues: 21.8767 Evaluate side-chains 78 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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: 1.9990 chunk 138 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 31 HIS M 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.071250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.040670 restraints weight = 209677.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040962 restraints weight = 113067.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041525 restraints weight = 71117.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.041561 restraints weight = 54821.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041589 restraints weight = 48593.591| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.9279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20343 Z= 0.159 Angle : 0.635 11.662 28958 Z= 0.359 Chirality : 0.045 0.331 3247 Planarity : 0.004 0.049 2533 Dihedral : 30.160 178.738 5455 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 0.95 (0.21), residues: 1530 helix: 1.49 (0.20), residues: 629 sheet: 0.52 (0.30), residues: 288 loop : -0.12 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 290 TYR 0.028 0.002 TYR F 88 PHE 0.016 0.002 PHE E 67 TRP 0.005 0.001 TRP K 146 HIS 0.006 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (20343) covalent geometry : angle 0.63470 / 0.36 (28958) hydrogen bonds : bond 0.05637 / 3.80 ( 1059) hydrogen bonds : angle 4.10490 / 3.07 ( 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 114 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8668 (tp30) cc_final: 0.8049 (tp30) REVERT: A 84 PHE cc_start: 0.9119 (m-10) cc_final: 0.8685 (m-10) REVERT: A 105 GLU cc_start: 0.9340 (tp30) cc_final: 0.9062 (tm-30) REVERT: A 120 MET cc_start: 0.8038 (mmm) cc_final: 0.7578 (mmm) REVERT: B 53 GLU cc_start: 0.9484 (mp0) cc_final: 0.9095 (pm20) REVERT: B 63 GLU cc_start: 0.9329 (pt0) cc_final: 0.8831 (pp20) REVERT: B 68 ASP cc_start: 0.9242 (m-30) cc_final: 0.9024 (m-30) REVERT: E 90 MET cc_start: 0.9330 (mmm) cc_final: 0.9110 (mmm) REVERT: F 50 ILE cc_start: 0.8904 (mm) cc_final: 0.8616 (mm) REVERT: F 63 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8917 (mt-10) REVERT: F 84 MET cc_start: 0.8746 (tpp) cc_final: 0.8459 (tpp) REVERT: H 56 MET cc_start: 0.9357 (mmp) cc_final: 0.9098 (mmm) REVERT: K 202 ARG cc_start: 0.5440 (tmt170) cc_final: 0.5218 (tpt90) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1553 time to fit residues: 27.1343 Evaluate side-chains 76 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 8.9990 chunk 104 optimal weight: 50.0000 chunk 106 optimal weight: 0.0470 chunk 9 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.070826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.040914 restraints weight = 211821.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.039549 restraints weight = 124747.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.040019 restraints weight = 79178.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040045 restraints weight = 59503.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.040153 restraints weight = 51937.191| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.9505 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= 0.163 Angle : 0.644 12.081 28958 Z= 0.366 Chirality : 0.044 0.323 3247 Planarity : 0.004 0.043 2533 Dihedral : 29.973 179.393 5455 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 1.00 (0.21), residues: 1530 helix: 1.43 (0.20), residues: 630 sheet: 0.83 (0.31), residues: 264 loop : -0.10 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 290 TYR 0.019 0.002 TYR G 50 PHE 0.014 0.001 PHE A 104 TRP 0.005 0.001 TRP K 146 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (20343) covalent geometry : angle 0.64420 / 0.37 (28958) hydrogen bonds : bond 0.06296 / 4.25 ( 1059) hydrogen bonds : angle 4.11058 / 3.06 ( 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 100 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8708 (tp30) cc_final: 0.8116 (tp30) REVERT: A 84 PHE cc_start: 0.9152 (m-10) cc_final: 0.8707 (m-10) REVERT: A 105 GLU cc_start: 0.9419 (tp30) cc_final: 0.9063 (tm-30) REVERT: A 120 MET cc_start: 0.7990 (mmm) cc_final: 0.7529 (mmm) REVERT: B 53 GLU cc_start: 0.9471 (mp0) cc_final: 0.9131 (pm20) REVERT: B 63 GLU cc_start: 0.9345 (pt0) cc_final: 0.8864 (pp20) REVERT: B 68 ASP cc_start: 0.9248 (m-30) cc_final: 0.9031 (m-30) REVERT: D 56 MET cc_start: 0.9240 (tpt) cc_final: 0.8797 (tpp) REVERT: E 90 MET cc_start: 0.9373 (mmm) cc_final: 0.9127 (mmm) REVERT: E 105 GLU cc_start: 0.9100 (pp20) cc_final: 0.8873 (pp20) REVERT: F 63 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8905 (mt-10) REVERT: F 68 ASP cc_start: 0.9221 (m-30) cc_final: 0.9013 (m-30) REVERT: F 84 MET cc_start: 0.8791 (tpp) cc_final: 0.8502 (tpp) REVERT: K 202 ARG cc_start: 0.5465 (tmt170) cc_final: 0.5230 (tpt90) REVERT: K 246 MET cc_start: 0.3762 (ptp) cc_final: 0.3213 (ptp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1402 time to fit residues: 22.1315 Evaluate side-chains 76 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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: 50.0000 chunk 97 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 86 optimal weight: 50.0000 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 151 optimal weight: 0.0670 overall best weight: 4.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 31 HIS ** F 75 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 = 0.3625 r_free = 0.3625 target = 0.070762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.040187 restraints weight = 211283.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040037 restraints weight = 113180.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040210 restraints weight = 76539.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040296 restraints weight = 61518.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040449 restraints weight = 55733.263| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.9748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20343 Z= 0.148 Angle : 0.616 11.611 28958 Z= 0.349 Chirality : 0.044 0.315 3247 Planarity : 0.004 0.040 2533 Dihedral : 29.893 178.721 5455 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 1.10 (0.21), residues: 1530 helix: 1.65 (0.20), residues: 628 sheet: 0.86 (0.31), residues: 264 loop : -0.19 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 290 TYR 0.028 0.002 TYR H 80 PHE 0.017 0.001 PHE E 104 TRP 0.004 0.001 TRP K 146 HIS 0.007 0.001 HIS N 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (20343) covalent geometry : angle 0.61622 / 0.35 (28958) hydrogen bonds : bond 0.05384 / 3.62 ( 1059) hydrogen bonds : angle 3.99241 / 2.97 ( 2621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5371.75 seconds wall clock time: 92 minutes 32.90 seconds (5552.90 seconds total)