Starting phenix.real_space_refine on Sat Sep 12 20:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzz_33535/09_2026/7xzz_33535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzz_33535/09_2026/7xzz_33535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xzz_33535/09_2026/7xzz_33535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzz_33535/09_2026/7xzz_33535_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xzz_33535/09_2026/7xzz_33535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzz_33535/09_2026/7xzz_33535.map" } resolution = 4.07 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= 0.000 sd= 0.002 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 309 5.49 5 S 78 5.16 5 C 10646 2.51 5 N 3495 2.21 5 O 4095 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: 18623 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: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3164 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3183 Classifications: {'DNA': 155} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 154} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen planarities: 3 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: 3.92, per 1000 atoms: 0.21 Number of scatterers: 18623 At special positions: 0 Unit cell: (159, 179.14, 120.84, 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 309 15.00 O 4095 8.00 N 3495 7.00 C 10646 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: 1.71 Conformation dependent library (CDL) restraints added in 537.2 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 149 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 2.48 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: 4.293A 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: 3.995A 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: 3.538A 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: 4.269A 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: 3.524A 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: 7.082A 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: 4.632A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.147A 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: 6.389A 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: 3.803A 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: 4.844A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.388A 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: 3.839A 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: 385 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 2.26 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: 3607 1.33 - 1.46: 6509 1.46 - 1.59: 8773 1.59 - 1.71: 615 1.71 - 1.84: 112 Bond restraints: 19616 Sorted by residual: bond pdb=" C3' DC I 121 " pdb=" C2' DC I 121 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.51e+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=" C PRO M 222 " pdb=" O PRO M 222 " ideal model delta sigma weight residual 1.240 1.202 0.039 1.12e-02 7.97e+03 1.19e+01 bond pdb=" C3' DC I 10 " pdb=" C2' DC I 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" CA PRO K 190 " pdb=" C PRO K 190 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.15e+01 ... (remaining 19611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 25437 1.73 - 3.45: 2169 3.45 - 5.18: 207 5.18 - 6.91: 24 6.91 - 8.63: 3 Bond angle restraints: 27840 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 108.00 112.10 -4.10 7.00e-01 2.04e+00 3.44e+01 angle pdb=" O5' DC I 144 " pdb=" C5' DC I 144 " pdb=" C4' DC I 144 " ideal model delta sigma weight residual 109.40 113.46 -4.06 8.00e-01 1.56e+00 2.57e+01 angle pdb=" O4' DA I 27 " pdb=" C4' DA I 27 " pdb=" C3' DA I 27 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" C3' DA I 131 " pdb=" C2' DA I 131 " pdb=" C1' DA I 131 " ideal model delta sigma weight residual 102.50 96.58 5.92 1.20e+00 6.94e-01 2.44e+01 angle pdb=" C3' DA J 36 " pdb=" C2' DA J 36 " pdb=" C1' DA J 36 " ideal model delta sigma weight residual 102.50 96.59 5.91 1.20e+00 6.94e-01 2.43e+01 ... (remaining 27835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.69: 9129 30.69 - 61.38: 1874 61.38 - 92.07: 67 92.07 - 122.76: 1 122.76 - 153.45: 1 Dihedral angle restraints: 11072 sinusoidal: 6568 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 66.55 153.45 1 3.50e+01 8.16e-04 1.48e+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 -161.76 -18.24 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 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2112 0.052 - 0.103: 732 0.103 - 0.155: 192 0.155 - 0.206: 76 0.206 - 0.258: 7 Chirality restraints: 3119 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 1.66e+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 1.50e+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 1.32e+00 ... (remaining 3116 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+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 3.04e-02 9.27e+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' DA J 19 " 0.030 2.00e-02 2.50e+03 1.26e-02 4.36e+00 pdb=" N9 DA J 19 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 19 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DA J 19 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA J 19 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DA J 19 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA J 19 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA J 19 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 19 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA J 19 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA J 19 " -0.004 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 37 2.35 - 2.99: 9024 2.99 - 3.63: 30316 3.63 - 4.26: 49078 4.26 - 4.90: 72886 Nonbonded interactions: 161341 Sorted by model distance: nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" NH2 ARG G 17 " pdb=" OP2 DA J 55 " model vdw 1.839 3.120 nonbonded pdb=" NH2 ARG K 202 " pdb=" OE2 GLU K 221 " model vdw 1.930 3.120 nonbonded pdb=" NH2 ARG F 36 " pdb=" OP1 DA J 85 " model vdw 1.962 3.120 nonbonded pdb=" NH2 ARG G 42 " pdb=" O4' DT I 110 " model vdw 1.980 3.120 ... (remaining 161336 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.190 Find NCS groups from input model: 0.250 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4317 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 0.058 19616 Z= 0.513 Angle : 0.981 8.632 27840 Z= 0.766 Chirality : 0.060 0.258 3119 Planarity : 0.005 0.045 2501 Dihedral : 25.147 153.453 8172 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 11.14 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 : 0.30 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 267 TYR 0.026 0.003 TYR B 88 PHE 0.018 0.002 PHE N 270 TRP 0.004 0.002 TRP N 146 HIS 0.010 0.002 HIS K 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.51 (19616) covalent geometry : angle 0.98135 / 0.77 (27840) hydrogen bonds : bond 0.11363 / 7.87 ( 1015) hydrogen bonds : angle 5.24993 / 3.83 ( 2529) *********************** 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 263 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.569 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 61 LEU cc_start: 0.8591 (mt) cc_final: 0.8295 (mt) REVERT: A 106 ASP cc_start: 0.8379 (m-30) cc_final: 0.7713 (m-30) REVERT: C 83 LEU cc_start: 0.9529 (mt) cc_final: 0.9047 (mt) REVERT: C 90 ASP cc_start: 0.8989 (t0) cc_final: 0.8760 (t0) REVERT: E 106 ASP cc_start: 0.8567 (m-30) cc_final: 0.7538 (m-30) REVERT: F 68 ASP cc_start: 0.8981 (m-30) cc_final: 0.8700 (p0) REVERT: F 97 LEU cc_start: 0.8977 (tp) cc_final: 0.8683 (tt) REVERT: G 38 ASN cc_start: 0.8115 (m-40) cc_final: 0.7859 (t0) REVERT: G 56 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8229 (mt-10) REVERT: G 64 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8154 (tm-30) outliers start: 2 outliers final: 0 residues processed: 261 average time/residue: 0.1516 time to fit residues: 59.6915 Evaluate side-chains 139 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.0470 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS K 178 HIS K 268 ASN K 288 ASN L 268 ASN L 288 ASN M 288 ASN N 168 HIS N 268 ASN N 288 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.082713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.047091 restraints weight = 128373.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.047918 restraints weight = 59308.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048095 restraints weight = 36639.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.048580 restraints weight = 28840.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.048736 restraints weight = 23820.247| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 19616 Z= 0.163 Angle : 0.700 9.312 27840 Z= 0.394 Chirality : 0.049 0.236 3119 Planarity : 0.005 0.113 2501 Dihedral : 29.244 157.692 5115 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.22 % Allowed : 3.19 % Favored : 96.59 % 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: 1.28 (0.20), residues: 1530 helix: 1.51 (0.19), residues: 625 sheet: 0.41 (0.26), residues: 328 loop : 0.57 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 95 TYR 0.027 0.002 TYR F 88 PHE 0.036 0.002 PHE G 25 TRP 0.009 0.002 TRP K 146 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (19616) covalent geometry : angle 0.70035 / 0.39 (27840) hydrogen bonds : bond 0.05379 / 3.74 ( 1015) hydrogen bonds : angle 4.26550 / 3.18 ( 2529) *********************** 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 187 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.569 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 50 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9412 (mm-30) REVERT: A 84 PHE cc_start: 0.8965 (m-80) cc_final: 0.8744 (m-80) REVERT: A 90 MET cc_start: 0.9604 (mmm) cc_final: 0.9391 (mmm) REVERT: A 93 GLN cc_start: 0.9427 (tt0) cc_final: 0.8878 (tp40) REVERT: A 106 ASP cc_start: 0.8956 (m-30) cc_final: 0.8440 (t70) REVERT: C 90 ASP cc_start: 0.8631 (t0) cc_final: 0.8306 (t0) REVERT: C 102 ILE cc_start: 0.9366 (mm) cc_final: 0.9083 (mp) REVERT: E 94 GLU cc_start: 0.9027 (tp30) cc_final: 0.8688 (tp30) REVERT: E 103 LEU cc_start: 0.9719 (tt) cc_final: 0.9485 (pp) REVERT: E 105 GLU cc_start: 0.8604 (pp20) cc_final: 0.8370 (pp20) REVERT: E 106 ASP cc_start: 0.8532 (m-30) cc_final: 0.8192 (m-30) REVERT: E 120 MET cc_start: 0.7714 (mpp) cc_final: 0.7132 (mpp) REVERT: G 38 ASN cc_start: 0.8726 (m-40) cc_final: 0.8051 (t0) REVERT: G 51 LEU cc_start: 0.9865 (tt) cc_final: 0.9467 (pp) REVERT: G 64 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8799 (tm-30) REVERT: G 90 ASP cc_start: 0.8434 (t70) cc_final: 0.8098 (t0) REVERT: K 193 HIS cc_start: 0.1035 (t-90) cc_final: 0.0726 (t-90) REVERT: M 224 GLU cc_start: 0.1737 (mp0) cc_final: 0.1108 (pm20) REVERT: N 237 MET cc_start: 0.8107 (mmm) cc_final: 0.7736 (mmm) outliers start: 3 outliers final: 0 residues processed: 184 average time/residue: 0.1417 time to fit residues: 39.7703 Evaluate side-chains 132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 155 optimal weight: 9.9990 chunk 87 optimal weight: 50.0000 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 112 optimal weight: 0.5980 chunk 131 optimal weight: 40.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN N 168 HIS N 214 HIS N 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.080754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.045325 restraints weight = 128291.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.045916 restraints weight = 58772.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046031 restraints weight = 36291.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.046534 restraints weight = 28662.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.046682 restraints weight = 23815.562| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 19616 Z= 0.160 Angle : 0.639 10.784 27840 Z= 0.365 Chirality : 0.046 0.218 3119 Planarity : 0.004 0.054 2501 Dihedral : 29.220 157.988 5115 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.15 % Allowed : 2.75 % Favored : 97.10 % 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: 1.43 (0.20), residues: 1530 helix: 1.58 (0.20), residues: 624 sheet: 0.62 (0.27), residues: 328 loop : 0.62 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.038 0.001 TYR B 88 PHE 0.016 0.001 PHE G 25 TRP 0.007 0.001 TRP K 146 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (19616) covalent geometry : angle 0.63877 / 0.36 (27840) hydrogen bonds : bond 0.05095 / 3.55 ( 1015) hydrogen bonds : angle 4.07192 / 3.02 ( 2529) *********************** 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 185 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.567 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 50 GLU cc_start: 0.9664 (mm-30) cc_final: 0.9437 (mm-30) REVERT: A 84 PHE cc_start: 0.9104 (m-80) cc_final: 0.8836 (m-80) REVERT: A 90 MET cc_start: 0.9634 (mmm) cc_final: 0.9376 (mmm) REVERT: A 93 GLN cc_start: 0.9442 (tt0) cc_final: 0.8612 (tp40) REVERT: A 94 GLU cc_start: 0.9406 (mm-30) cc_final: 0.8960 (tp30) REVERT: A 97 GLU cc_start: 0.8930 (pp20) cc_final: 0.8727 (pp20) REVERT: A 106 ASP cc_start: 0.9018 (m-30) cc_final: 0.8504 (t70) REVERT: B 63 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.9017 (pm20) REVERT: B 68 ASP cc_start: 0.9108 (m-30) cc_final: 0.8796 (m-30) REVERT: B 84 MET cc_start: 0.9107 (tpt) cc_final: 0.8780 (tpp) REVERT: C 90 ASP cc_start: 0.8561 (t0) cc_final: 0.8301 (t0) REVERT: C 102 ILE cc_start: 0.9359 (mm) cc_final: 0.9094 (mp) REVERT: D 68 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9230 (mm-30) REVERT: D 110 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8449 (mt-10) REVERT: E 67 PHE cc_start: 0.9447 (t80) cc_final: 0.9158 (t80) REVERT: E 106 ASP cc_start: 0.8600 (m-30) cc_final: 0.8263 (m-30) REVERT: E 120 MET cc_start: 0.7643 (mpp) cc_final: 0.7093 (mpp) REVERT: F 63 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9197 (mp0) REVERT: F 84 MET cc_start: 0.9593 (mmp) cc_final: 0.9383 (tpp) REVERT: G 38 ASN cc_start: 0.8890 (m-40) cc_final: 0.8120 (t0) REVERT: G 51 LEU cc_start: 0.9875 (tt) cc_final: 0.9483 (pp) REVERT: G 64 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8891 (tm-30) REVERT: G 72 ASP cc_start: 0.8987 (m-30) cc_final: 0.8734 (m-30) REVERT: G 90 ASP cc_start: 0.8506 (t70) cc_final: 0.8004 (t0) REVERT: H 59 MET cc_start: 0.9772 (tpp) cc_final: 0.9374 (mmp) REVERT: N 237 MET cc_start: 0.7988 (mmm) cc_final: 0.7631 (mmm) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.1449 time to fit residues: 40.7718 Evaluate side-chains 132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 119 optimal weight: 10.0000 chunk 84 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 172 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 overall best weight: 5.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS H 46 HIS K 100 GLN L 239 ASN M 193 HIS M 239 ASN N 168 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.074688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038444 restraints weight = 132800.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.038822 restraints weight = 70105.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038988 restraints weight = 46076.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039313 restraints weight = 36757.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039561 restraints weight = 31861.803| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 19616 Z= 0.265 Angle : 0.763 8.936 27840 Z= 0.425 Chirality : 0.048 0.231 3119 Planarity : 0.006 0.054 2501 Dihedral : 29.555 162.257 5115 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.22 % Allowed : 4.31 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1530 helix: 1.13 (0.19), residues: 615 sheet: 0.78 (0.29), residues: 304 loop : 0.47 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 134 TYR 0.024 0.002 TYR B 51 PHE 0.018 0.002 PHE F 100 TRP 0.009 0.001 TRP K 146 HIS 0.027 0.003 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.27 (19616) covalent geometry : angle 0.76322 / 0.42 (27840) hydrogen bonds : bond 0.07977 / 5.47 ( 1015) hydrogen bonds : angle 4.44004 / 3.25 ( 2529) *********************** 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 147 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.529 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 50 GLU cc_start: 0.9594 (mm-30) cc_final: 0.9363 (mm-30) REVERT: A 51 ILE cc_start: 0.9669 (mt) cc_final: 0.9467 (mm) REVERT: A 90 MET cc_start: 0.9604 (mmm) cc_final: 0.9341 (mmp) REVERT: A 94 GLU cc_start: 0.9557 (mm-30) cc_final: 0.8833 (mm-30) REVERT: A 97 GLU cc_start: 0.9122 (pp20) cc_final: 0.8756 (pp20) REVERT: A 105 GLU cc_start: 0.9460 (tm-30) cc_final: 0.9238 (tm-30) REVERT: A 106 ASP cc_start: 0.8883 (m-30) cc_final: 0.8388 (m-30) REVERT: B 34 ILE cc_start: 0.9772 (mt) cc_final: 0.9559 (tt) REVERT: B 68 ASP cc_start: 0.9066 (m-30) cc_final: 0.8820 (m-30) REVERT: B 84 MET cc_start: 0.9389 (tpt) cc_final: 0.8963 (tpp) REVERT: C 90 ASP cc_start: 0.9002 (t0) cc_final: 0.8688 (t0) REVERT: D 59 MET cc_start: 0.9613 (mmm) cc_final: 0.9293 (mmm) REVERT: D 68 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9181 (mm-30) REVERT: E 92 LEU cc_start: 0.9570 (tp) cc_final: 0.9252 (tt) REVERT: E 94 GLU cc_start: 0.9740 (tp30) cc_final: 0.9287 (tp30) REVERT: E 96 CYS cc_start: 0.9309 (m) cc_final: 0.8847 (m) REVERT: E 106 ASP cc_start: 0.8791 (m-30) cc_final: 0.8552 (m-30) REVERT: G 64 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8903 (tm-30) REVERT: G 75 LYS cc_start: 0.8706 (mmpt) cc_final: 0.8402 (mmmt) REVERT: G 90 ASP cc_start: 0.8604 (t70) cc_final: 0.8400 (t70) REVERT: H 59 MET cc_start: 0.9740 (tpp) cc_final: 0.9421 (mmp) REVERT: H 97 LEU cc_start: 0.9663 (mt) cc_final: 0.9453 (mt) REVERT: K 246 MET cc_start: -0.0418 (mtt) cc_final: -0.0811 (mtm) REVERT: L 169 MET cc_start: 0.0766 (tpp) cc_final: 0.0286 (tpt) outliers start: 3 outliers final: 0 residues processed: 144 average time/residue: 0.1484 time to fit residues: 32.5427 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 : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 94 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 18 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 130 optimal weight: 0.5980 chunk 97 optimal weight: 30.0000 chunk 136 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 154 optimal weight: 50.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 68 ASN H 46 HIS L 168 HIS ** M 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 HIS N 168 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.075772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.039200 restraints weight = 130744.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.039883 restraints weight = 60057.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040163 restraints weight = 37938.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.040464 restraints weight = 28709.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040512 restraints weight = 24850.526| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 19616 Z= 0.165 Angle : 0.636 7.812 27840 Z= 0.360 Chirality : 0.046 0.240 3119 Planarity : 0.005 0.061 2501 Dihedral : 29.567 164.115 5115 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 1.33 (0.21), residues: 1530 helix: 1.51 (0.20), residues: 619 sheet: 0.86 (0.29), residues: 304 loop : 0.39 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 196 TYR 0.015 0.002 TYR G 39 PHE 0.028 0.001 PHE E 104 TRP 0.007 0.001 TRP K 146 HIS 0.010 0.001 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (19616) covalent geometry : angle 0.63641 / 0.36 (27840) hydrogen bonds : bond 0.05116 / 3.53 ( 1015) hydrogen bonds : angle 4.06205 / 2.98 ( 2529) *********************** 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 154 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.557 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: A 50 GLU cc_start: 0.9595 (mm-30) cc_final: 0.9321 (mm-30) REVERT: A 51 ILE cc_start: 0.9633 (mt) cc_final: 0.9427 (mm) REVERT: A 90 MET cc_start: 0.9614 (mmm) cc_final: 0.9385 (mmm) REVERT: A 94 GLU cc_start: 0.9573 (mm-30) cc_final: 0.8802 (mm-30) REVERT: A 97 GLU cc_start: 0.9166 (pp20) cc_final: 0.8821 (pp20) REVERT: A 105 GLU cc_start: 0.9472 (tm-30) cc_final: 0.9236 (tm-30) REVERT: A 106 ASP cc_start: 0.8989 (m-30) cc_final: 0.8537 (m-30) REVERT: B 63 GLU cc_start: 0.9130 (pp20) cc_final: 0.8920 (pp20) REVERT: B 68 ASP cc_start: 0.9087 (m-30) cc_final: 0.8815 (m-30) REVERT: B 84 MET cc_start: 0.9407 (tpt) cc_final: 0.8989 (mmm) REVERT: C 90 ASP cc_start: 0.9049 (t0) cc_final: 0.8666 (t0) REVERT: D 65 ASP cc_start: 0.9329 (t0) cc_final: 0.9034 (t0) REVERT: E 92 LEU cc_start: 0.9468 (tp) cc_final: 0.9114 (tt) REVERT: E 96 CYS cc_start: 0.9322 (m) cc_final: 0.8806 (m) REVERT: E 106 ASP cc_start: 0.8805 (m-30) cc_final: 0.8488 (m-30) REVERT: E 120 MET cc_start: 0.8875 (mmp) cc_final: 0.8517 (mmm) REVERT: G 64 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8839 (tm-30) REVERT: G 68 ASN cc_start: 0.8973 (m-40) cc_final: 0.8596 (m110) REVERT: G 72 ASP cc_start: 0.9049 (m-30) cc_final: 0.8821 (m-30) REVERT: G 75 LYS cc_start: 0.8714 (mmpt) cc_final: 0.8418 (mmmm) REVERT: G 90 ASP cc_start: 0.8513 (t70) cc_final: 0.8281 (t70) REVERT: H 59 MET cc_start: 0.9744 (tpp) cc_final: 0.9512 (mmm) REVERT: K 236 TYR cc_start: 0.5742 (m-80) cc_final: 0.5500 (m-80) REVERT: K 246 MET cc_start: -0.0480 (mtt) cc_final: -0.0997 (mtm) REVERT: L 169 MET cc_start: 0.0357 (tpp) cc_final: 0.0137 (tpp) REVERT: N 237 MET cc_start: 0.8027 (mmm) cc_final: 0.7759 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1449 time to fit residues: 34.3765 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 : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 175 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 136 optimal weight: 40.0000 chunk 154 optimal weight: 50.0000 chunk 125 optimal weight: 50.0000 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN K 233 HIS N 168 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.073430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036304 restraints weight = 134547.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.036828 restraints weight = 65248.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036982 restraints weight = 41439.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.037240 restraints weight = 31880.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037285 restraints weight = 27436.383| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 19616 Z= 0.203 Angle : 0.679 8.733 27840 Z= 0.378 Chirality : 0.046 0.257 3119 Planarity : 0.005 0.053 2501 Dihedral : 29.563 166.906 5115 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: 1.37 (0.21), residues: 1530 helix: 1.58 (0.20), residues: 619 sheet: 0.86 (0.29), residues: 304 loop : 0.36 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 196 TYR 0.021 0.002 TYR B 51 PHE 0.032 0.002 PHE A 104 TRP 0.006 0.001 TRP L 146 HIS 0.013 0.002 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (19616) covalent geometry : angle 0.67943 / 0.38 (27840) hydrogen bonds : bond 0.05946 / 4.10 ( 1015) hydrogen bonds : angle 4.09024 / 3.01 ( 2529) *********************** 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 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9321 (mm-30) REVERT: A 51 ILE cc_start: 0.9671 (mt) cc_final: 0.9469 (mm) REVERT: A 94 GLU cc_start: 0.9609 (mm-30) cc_final: 0.8815 (mm-30) REVERT: A 97 GLU cc_start: 0.9157 (pp20) cc_final: 0.8777 (pp20) REVERT: A 105 GLU cc_start: 0.9498 (tm-30) cc_final: 0.9269 (tm-30) REVERT: A 106 ASP cc_start: 0.8928 (m-30) cc_final: 0.8485 (m-30) REVERT: B 68 ASP cc_start: 0.9190 (m-30) cc_final: 0.8921 (m-30) REVERT: B 84 MET cc_start: 0.9446 (tpt) cc_final: 0.9001 (mmm) REVERT: C 90 ASP cc_start: 0.8995 (t0) cc_final: 0.8670 (t0) REVERT: D 65 ASP cc_start: 0.9331 (t0) cc_final: 0.9048 (t0) REVERT: E 92 LEU cc_start: 0.9484 (tp) cc_final: 0.9132 (tt) REVERT: E 96 CYS cc_start: 0.9349 (m) cc_final: 0.8874 (m) REVERT: E 106 ASP cc_start: 0.8836 (m-30) cc_final: 0.8546 (m-30) REVERT: E 120 MET cc_start: 0.9012 (mmp) cc_final: 0.8743 (mmm) REVERT: F 63 GLU cc_start: 0.9546 (mt-10) cc_final: 0.9269 (mp0) REVERT: F 84 MET cc_start: 0.9370 (tpp) cc_final: 0.8882 (tpp) REVERT: G 64 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8948 (tm-30) REVERT: G 68 ASN cc_start: 0.9116 (m-40) cc_final: 0.8788 (m110) REVERT: G 75 LYS cc_start: 0.8764 (mmpt) cc_final: 0.8359 (mmmm) REVERT: G 90 ASP cc_start: 0.8494 (t70) cc_final: 0.8260 (t70) REVERT: H 59 MET cc_start: 0.9741 (tpp) cc_final: 0.9529 (mmm) REVERT: K 246 MET cc_start: -0.0233 (mtt) cc_final: -0.0591 (mtm) REVERT: L 169 MET cc_start: 0.0423 (tpp) cc_final: 0.0206 (tpp) REVERT: N 237 MET cc_start: 0.8043 (mmm) cc_final: 0.7795 (mmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1509 time to fit residues: 33.0515 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 : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.074598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038002 restraints weight = 131196.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038448 restraints weight = 62183.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.038595 restraints weight = 37956.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.038932 restraints weight = 29901.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.039029 restraints weight = 25259.792| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19616 Z= 0.137 Angle : 0.614 8.546 27840 Z= 0.348 Chirality : 0.045 0.273 3119 Planarity : 0.004 0.054 2501 Dihedral : 29.526 169.106 5115 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 1.49 (0.21), residues: 1530 helix: 1.76 (0.20), residues: 618 sheet: 0.86 (0.30), residues: 300 loop : 0.36 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 175 TYR 0.039 0.001 TYR H 80 PHE 0.013 0.001 PHE F 61 TRP 0.004 0.001 TRP K 146 HIS 0.011 0.001 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (19616) covalent geometry : angle 0.61426 / 0.35 (27840) hydrogen bonds : bond 0.04503 / 3.12 ( 1015) hydrogen bonds : angle 3.87121 / 2.86 ( 2529) *********************** 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 156 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.560 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 50 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9393 (mm-30) REVERT: A 51 ILE cc_start: 0.9518 (mt) cc_final: 0.9312 (mm) REVERT: A 94 GLU cc_start: 0.9618 (mm-30) cc_final: 0.8910 (mm-30) REVERT: A 97 GLU cc_start: 0.9226 (pp20) cc_final: 0.8840 (pp20) REVERT: A 105 GLU cc_start: 0.9546 (tm-30) cc_final: 0.9338 (tm-30) REVERT: A 106 ASP cc_start: 0.9037 (m-30) cc_final: 0.8680 (m-30) REVERT: A 120 MET cc_start: 0.8662 (mmp) cc_final: 0.8370 (mmm) REVERT: B 63 GLU cc_start: 0.9252 (pp20) cc_final: 0.9031 (pp20) REVERT: B 68 ASP cc_start: 0.9245 (m-30) cc_final: 0.8992 (m-30) REVERT: B 84 MET cc_start: 0.9414 (tpt) cc_final: 0.9193 (mmm) REVERT: C 90 ASP cc_start: 0.8690 (t0) cc_final: 0.8393 (t0) REVERT: D 65 ASP cc_start: 0.9300 (t0) cc_final: 0.9030 (t0) REVERT: E 92 LEU cc_start: 0.9446 (tp) cc_final: 0.9099 (tp) REVERT: E 94 GLU cc_start: 0.9660 (tp30) cc_final: 0.9145 (tp30) REVERT: E 96 CYS cc_start: 0.9318 (m) cc_final: 0.8930 (m) REVERT: E 106 ASP cc_start: 0.8970 (m-30) cc_final: 0.8678 (m-30) REVERT: E 120 MET cc_start: 0.8751 (mmp) cc_final: 0.8472 (mmm) REVERT: F 63 GLU cc_start: 0.9559 (mt-10) cc_final: 0.9276 (mp0) REVERT: G 64 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8976 (tm-30) REVERT: G 68 ASN cc_start: 0.9134 (m-40) cc_final: 0.8814 (m110) REVERT: G 75 LYS cc_start: 0.8628 (mmpt) cc_final: 0.8325 (mmmm) REVERT: G 90 ASP cc_start: 0.8271 (t70) cc_final: 0.8070 (t0) REVERT: H 59 MET cc_start: 0.9812 (tpp) cc_final: 0.9570 (mmm) REVERT: L 169 MET cc_start: 0.0841 (tpp) cc_final: 0.0636 (tpp) REVERT: N 133 MET cc_start: 0.6752 (ppp) cc_final: 0.6381 (ppp) REVERT: N 237 MET cc_start: 0.8036 (mmm) cc_final: 0.7826 (mmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1431 time to fit residues: 34.7586 Evaluate side-chains 117 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 130 optimal weight: 0.0060 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 24 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037513 restraints weight = 130653.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.037858 restraints weight = 60939.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038344 restraints weight = 40073.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.038368 restraints weight = 30689.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.038477 restraints weight = 25776.276| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19616 Z= 0.129 Angle : 0.608 8.631 27840 Z= 0.344 Chirality : 0.044 0.281 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.433 170.821 5115 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 1.49 (0.21), residues: 1530 helix: 1.78 (0.20), residues: 617 sheet: 0.88 (0.29), residues: 300 loop : 0.36 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 175 TYR 0.032 0.001 TYR H 80 PHE 0.019 0.001 PHE C 25 TRP 0.004 0.001 TRP K 146 HIS 0.011 0.001 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (19616) covalent geometry : angle 0.60829 / 0.34 (27840) hydrogen bonds : bond 0.04359 / 3.01 ( 1015) hydrogen bonds : angle 3.78201 / 2.77 ( 2529) *********************** 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 156 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.529 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: A 50 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9392 (mm-30) REVERT: A 84 PHE cc_start: 0.8981 (m-80) cc_final: 0.8444 (m-80) REVERT: A 94 GLU cc_start: 0.9615 (mm-30) cc_final: 0.8892 (mm-30) REVERT: A 97 GLU cc_start: 0.9205 (pp20) cc_final: 0.8808 (pp20) REVERT: A 105 GLU cc_start: 0.9543 (tm-30) cc_final: 0.9332 (tm-30) REVERT: A 106 ASP cc_start: 0.9049 (m-30) cc_final: 0.8549 (m-30) REVERT: A 120 MET cc_start: 0.8698 (mmp) cc_final: 0.8362 (mmm) REVERT: B 68 ASP cc_start: 0.9239 (m-30) cc_final: 0.8988 (m-30) REVERT: B 84 MET cc_start: 0.9381 (tpt) cc_final: 0.9168 (mmm) REVERT: C 90 ASP cc_start: 0.8679 (t0) cc_final: 0.8376 (t0) REVERT: D 59 MET cc_start: 0.9706 (mmm) cc_final: 0.9305 (mmm) REVERT: D 65 ASP cc_start: 0.9320 (t0) cc_final: 0.9047 (t0) REVERT: E 92 LEU cc_start: 0.9424 (tp) cc_final: 0.9131 (tt) REVERT: E 96 CYS cc_start: 0.9307 (m) cc_final: 0.8855 (m) REVERT: E 106 ASP cc_start: 0.9224 (m-30) cc_final: 0.8510 (m-30) REVERT: G 64 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9002 (tm-30) REVERT: G 68 ASN cc_start: 0.9146 (m-40) cc_final: 0.8816 (m110) REVERT: G 75 LYS cc_start: 0.8766 (mmpt) cc_final: 0.8472 (mmmm) REVERT: G 90 ASP cc_start: 0.8254 (t70) cc_final: 0.8015 (t0) REVERT: H 59 MET cc_start: 0.9797 (tpp) cc_final: 0.9337 (mmm) REVERT: H 65 ASP cc_start: 0.9629 (t70) cc_final: 0.9392 (t0) REVERT: K 193 HIS cc_start: 0.2360 (t-90) cc_final: 0.1911 (t-90) REVERT: L 243 MET cc_start: 0.0157 (ppp) cc_final: -0.0082 (ppp) REVERT: N 133 MET cc_start: 0.6760 (ppp) cc_final: 0.6444 (ppp) REVERT: N 237 MET cc_start: 0.8077 (mmm) cc_final: 0.7875 (mmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1342 time to fit residues: 32.6538 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 : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 16 optimal weight: 0.8980 chunk 96 optimal weight: 30.0000 chunk 109 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 153 optimal weight: 40.0000 chunk 13 optimal weight: 0.9980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN N 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.072431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.036224 restraints weight = 133224.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.036507 restraints weight = 67425.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036679 restraints weight = 42353.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036907 restraints weight = 32695.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036966 restraints weight = 28231.299| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 19616 Z= 0.209 Angle : 0.674 10.899 27840 Z= 0.374 Chirality : 0.045 0.287 3119 Planarity : 0.004 0.054 2501 Dihedral : 29.564 174.398 5115 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 1.34 (0.21), residues: 1530 helix: 1.57 (0.20), residues: 624 sheet: 0.85 (0.29), residues: 304 loop : 0.32 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 196 TYR 0.036 0.002 TYR H 80 PHE 0.029 0.002 PHE E 104 TRP 0.005 0.001 TRP K 146 HIS 0.011 0.001 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 (19616) covalent geometry : angle 0.67449 / 0.37 (27840) hydrogen bonds : bond 0.05745 / 3.94 ( 1015) hydrogen bonds : angle 4.06034 / 2.98 ( 2529) *********************** 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 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.518 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: A 50 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9275 (mm-30) REVERT: A 51 ILE cc_start: 0.9660 (mt) cc_final: 0.9440 (mm) REVERT: A 84 PHE cc_start: 0.9117 (m-80) cc_final: 0.8587 (m-80) REVERT: A 94 GLU cc_start: 0.9592 (mm-30) cc_final: 0.8707 (mm-30) REVERT: A 97 GLU cc_start: 0.9160 (pp20) cc_final: 0.8779 (pp20) REVERT: A 106 ASP cc_start: 0.8780 (m-30) cc_final: 0.8389 (m-30) REVERT: A 120 MET cc_start: 0.9120 (mmp) cc_final: 0.8721 (mmm) REVERT: B 66 ILE cc_start: 0.9650 (tt) cc_final: 0.9437 (pt) REVERT: B 68 ASP cc_start: 0.9083 (m-30) cc_final: 0.8827 (m-30) REVERT: B 84 MET cc_start: 0.9437 (tpt) cc_final: 0.9186 (mmm) REVERT: C 90 ASP cc_start: 0.9063 (t0) cc_final: 0.8753 (t0) REVERT: D 65 ASP cc_start: 0.9382 (t0) cc_final: 0.9081 (t0) REVERT: E 92 LEU cc_start: 0.9490 (tp) cc_final: 0.9143 (tt) REVERT: E 94 GLU cc_start: 0.9218 (tp30) cc_final: 0.9018 (tp30) REVERT: E 96 CYS cc_start: 0.9312 (m) cc_final: 0.8876 (m) REVERT: F 84 MET cc_start: 0.9305 (tpp) cc_final: 0.8954 (tpp) REVERT: G 64 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8930 (tm-30) REVERT: G 68 ASN cc_start: 0.9094 (m-40) cc_final: 0.8714 (m-40) REVERT: G 90 ASP cc_start: 0.8519 (t70) cc_final: 0.8282 (t0) REVERT: H 59 MET cc_start: 0.9694 (tpp) cc_final: 0.9198 (mmm) REVERT: K 246 MET cc_start: -0.0564 (mtt) cc_final: -0.0831 (mtt) REVERT: N 133 MET cc_start: 0.6790 (ppp) cc_final: 0.6471 (ppp) REVERT: N 237 MET cc_start: 0.8001 (mmm) cc_final: 0.7780 (mmm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1433 time to fit residues: 32.3730 Evaluate side-chains 112 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 76 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN N 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.074042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037461 restraints weight = 129937.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037920 restraints weight = 61705.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.038197 restraints weight = 41371.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.038275 restraints weight = 30171.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038318 restraints weight = 25484.620| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19616 Z= 0.130 Angle : 0.624 11.619 27840 Z= 0.353 Chirality : 0.045 0.304 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.507 176.768 5115 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.42 (0.21), residues: 1530 helix: 1.69 (0.20), residues: 617 sheet: 0.85 (0.29), residues: 300 loop : 0.34 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 49 TYR 0.033 0.001 TYR H 80 PHE 0.014 0.001 PHE F 61 TRP 0.004 0.001 TRP K 146 HIS 0.010 0.001 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (19616) covalent geometry : angle 0.62417 / 0.35 (27840) hydrogen bonds : bond 0.04300 / 2.96 ( 1015) hydrogen bonds : angle 3.82428 / 2.81 ( 2529) ********************** 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 153 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.571 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 50 GLU cc_start: 0.9644 (mm-30) cc_final: 0.9344 (mm-30) REVERT: A 84 PHE cc_start: 0.9056 (m-80) cc_final: 0.8530 (m-80) REVERT: A 94 GLU cc_start: 0.9627 (mm-30) cc_final: 0.8861 (mm-30) REVERT: A 97 GLU cc_start: 0.9203 (pp20) cc_final: 0.8787 (pp20) REVERT: A 120 MET cc_start: 0.8780 (mmp) cc_final: 0.8386 (mmm) REVERT: B 68 ASP cc_start: 0.9215 (m-30) cc_final: 0.8934 (m-30) REVERT: B 84 MET cc_start: 0.9365 (tpt) cc_final: 0.9124 (mmm) REVERT: C 90 ASP cc_start: 0.8714 (t0) cc_final: 0.8408 (t0) REVERT: D 59 MET cc_start: 0.9705 (mmm) cc_final: 0.9316 (mmm) REVERT: E 92 LEU cc_start: 0.9433 (tp) cc_final: 0.9135 (tt) REVERT: E 96 CYS cc_start: 0.9291 (m) cc_final: 0.8862 (m) REVERT: G 64 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8987 (tm-30) REVERT: G 68 ASN cc_start: 0.9128 (m-40) cc_final: 0.8804 (m110) REVERT: G 75 LYS cc_start: 0.8803 (mmpt) cc_final: 0.8518 (mmmm) REVERT: G 90 ASP cc_start: 0.8268 (t70) cc_final: 0.8028 (t0) REVERT: H 59 MET cc_start: 0.9804 (tpp) cc_final: 0.9359 (mmm) REVERT: H 65 ASP cc_start: 0.9611 (t70) cc_final: 0.9397 (t0) REVERT: K 193 HIS cc_start: 0.2101 (t-90) cc_final: 0.1647 (t-90) REVERT: N 133 MET cc_start: 0.6715 (ppp) cc_final: 0.6446 (ppp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1400 time to fit residues: 33.3305 Evaluate side-chains 117 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 93 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.073890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036883 restraints weight = 131385.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.037317 restraints weight = 61270.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037792 restraints weight = 39957.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.038095 restraints weight = 30552.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.038179 restraints weight = 25847.804| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 19616 Z= 0.128 Angle : 0.606 9.989 27840 Z= 0.343 Chirality : 0.044 0.304 3119 Planarity : 0.004 0.054 2501 Dihedral : 29.434 178.139 5115 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 1.47 (0.21), residues: 1530 helix: 1.73 (0.20), residues: 619 sheet: 0.82 (0.29), residues: 300 loop : 0.40 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 69 TYR 0.030 0.001 TYR H 80 PHE 0.026 0.001 PHE E 104 TRP 0.004 0.001 TRP K 146 HIS 0.010 0.001 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (19616) covalent geometry : angle 0.60594 / 0.34 (27840) hydrogen bonds : bond 0.04274 / 2.96 ( 1015) hydrogen bonds : angle 3.77231 / 2.76 ( 2529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5285.33 seconds wall clock time: 91 minutes 10.11 seconds (5470.11 seconds total)