Starting phenix.real_space_refine on Sat Jul 4 04:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzz_33535/07_2026/7xzz_33535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzz_33535/07_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_33535/07_2026/7xzz_33535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzz_33535/07_2026/7xzz_33535_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xzz_33535/07_2026/7xzz_33535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzz_33535/07_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-dev-6108/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: 3.67, per 1000 atoms: 0.20 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: 1.57 Conformation dependent library (CDL) restraints added in 576.7 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: 2.79 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: 3.61 Time building geometry restraints manager: 2.07 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: 25459 1.73 - 3.45: 2153 3.45 - 5.18: 201 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.720 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- 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= 0.512 Angle : 0.976 8.632 27840 Z= 0.760 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 0.97602 / 0.76 (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 : 0.552 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: 0.8294 (mt) REVERT: A 106 ASP cc_start: 0.8379 (m-30) cc_final: 0.7712 (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: 0.1400 time to fit residues: 55.0209 Evaluate side-chains 140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 30.0000 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 = 0.3905 r_free = 0.3905 target = 0.082656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.047201 restraints weight = 128451.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.047502 restraints weight = 60352.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.047732 restraints weight = 37340.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.048186 restraints weight = 28981.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048484 restraints weight = 24038.328| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 19616 Z= 0.164 Angle : 0.689 9.830 27840 Z= 0.390 Chirality : 0.049 0.227 3119 Planarity : 0.005 0.108 2501 Dihedral : 29.297 157.818 5115 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.22 % Allowed : 3.04 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1530 helix: 1.51 (0.19), residues: 625 sheet: 0.42 (0.26), residues: 328 loop : 0.58 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 95 TYR 0.023 0.002 TYR F 88 PHE 0.035 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 0.00320 / 0.16 (19616) covalent geometry : angle 0.68894 / 0.39 (27840) hydrogen bonds : bond 0.05389 / 3.75 ( 1015) hydrogen bonds : angle 4.27141 / 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 : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9636 (mm-30) cc_final: 0.9416 (mm-30) REVERT: A 84 PHE cc_start: 0.8964 (m-80) cc_final: 0.8739 (m-80) REVERT: A 90 MET cc_start: 0.9604 (mmm) cc_final: 0.9396 (mmm) REVERT: A 93 GLN cc_start: 0.9429 (tt0) cc_final: 0.8885 (tp40) REVERT: A 106 ASP cc_start: 0.8964 (m-30) cc_final: 0.8443 (t70) REVERT: C 90 ASP cc_start: 0.8634 (t0) cc_final: 0.8300 (t0) REVERT: C 102 ILE cc_start: 0.9367 (mm) cc_final: 0.9078 (mp) REVERT: E 94 GLU cc_start: 0.9010 (tp30) cc_final: 0.8689 (tp30) REVERT: E 103 LEU cc_start: 0.9703 (tt) cc_final: 0.9456 (pp) REVERT: E 105 GLU cc_start: 0.8591 (pp20) cc_final: 0.8364 (pp20) REVERT: E 106 ASP cc_start: 0.8521 (m-30) cc_final: 0.8188 (m-30) REVERT: E 120 MET cc_start: 0.7673 (mpp) cc_final: 0.7105 (mpp) REVERT: G 38 ASN cc_start: 0.8728 (m-40) cc_final: 0.8051 (t0) REVERT: G 51 LEU cc_start: 0.9863 (tt) cc_final: 0.9465 (pp) REVERT: G 64 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8807 (tm-30) REVERT: G 90 ASP cc_start: 0.8421 (t70) cc_final: 0.8086 (t0) REVERT: K 193 HIS cc_start: 0.1148 (t-90) cc_final: 0.0844 (t-90) REVERT: M 224 GLU cc_start: 0.2010 (mp0) cc_final: 0.1357 (pm20) REVERT: N 237 MET cc_start: 0.8117 (mmm) cc_final: 0.7749 (mmm) outliers start: 3 outliers final: 0 residues processed: 184 average time/residue: 0.1361 time to fit residues: 38.1044 Evaluate side-chains 131 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 8.9990 chunk 87 optimal weight: 50.0000 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 131 optimal weight: 50.0000 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 HIS K 239 ASN N 168 HIS N 214 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.079859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043796 restraints weight = 128812.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.044597 restraints weight = 58897.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045134 restraints weight = 36803.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.045301 restraints weight = 27319.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.045248 restraints weight = 21647.030| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 19616 Z= 0.163 Angle : 0.635 7.648 27840 Z= 0.365 Chirality : 0.046 0.215 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.335 159.597 5115 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.15 % Allowed : 3.41 % Favored : 96.44 % 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 (0.20), residues: 1530 helix: 1.46 (0.20), residues: 624 sheet: 0.59 (0.27), residues: 328 loop : 0.61 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 95 TYR 0.030 0.002 TYR B 88 PHE 0.016 0.001 PHE G 25 TRP 0.008 0.001 TRP L 146 HIS 0.009 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (19616) covalent geometry : angle 0.63502 / 0.37 (27840) hydrogen bonds : bond 0.05192 / 3.61 ( 1015) hydrogen bonds : angle 4.07625 / 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 187 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.596 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: 0.9661 (mm-30) cc_final: 0.9433 (mm-30) REVERT: A 76 GLN cc_start: 0.9199 (mp10) cc_final: 0.8982 (pm20) REVERT: A 84 PHE cc_start: 0.9101 (m-80) cc_final: 0.8843 (m-80) REVERT: A 90 MET cc_start: 0.9665 (mmm) cc_final: 0.9332 (mmm) REVERT: A 93 GLN cc_start: 0.9386 (tt0) cc_final: 0.8489 (tp40) REVERT: A 105 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9221 (tm-30) REVERT: A 106 ASP cc_start: 0.8999 (m-30) cc_final: 0.8472 (m-30) REVERT: B 43 VAL cc_start: 0.9392 (t) cc_final: 0.9184 (t) REVERT: B 46 ILE cc_start: 0.9409 (mp) cc_final: 0.8954 (tp) REVERT: B 68 ASP cc_start: 0.9066 (m-30) cc_final: 0.8755 (m-30) REVERT: B 84 MET cc_start: 0.9033 (tpt) cc_final: 0.8709 (tpp) REVERT: C 83 LEU cc_start: 0.9670 (mt) cc_final: 0.9450 (mt) REVERT: C 90 ASP cc_start: 0.8689 (t0) cc_final: 0.8381 (t70) REVERT: C 102 ILE cc_start: 0.9404 (mm) cc_final: 0.9158 (mp) REVERT: D 68 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9247 (mm-30) REVERT: D 110 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8515 (mt-10) REVERT: E 67 PHE cc_start: 0.9470 (t80) cc_final: 0.9110 (t80) REVERT: E 94 GLU cc_start: 0.9024 (tp30) cc_final: 0.8751 (tp30) REVERT: E 106 ASP cc_start: 0.8609 (m-30) cc_final: 0.8256 (m-30) REVERT: F 63 GLU cc_start: 0.9523 (OUTLIER) cc_final: 0.9217 (mp0) REVERT: F 84 MET cc_start: 0.9391 (tpp) cc_final: 0.9071 (tpp) REVERT: G 38 ASN cc_start: 0.8944 (m-40) cc_final: 0.8239 (t0) REVERT: G 64 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8916 (tm-30) REVERT: G 72 ASP cc_start: 0.8937 (m-30) cc_final: 0.8681 (m-30) REVERT: G 90 ASP cc_start: 0.8412 (t70) cc_final: 0.8165 (t70) REVERT: H 59 MET cc_start: 0.9757 (tpp) cc_final: 0.9371 (mmp) REVERT: K 193 HIS cc_start: 0.0565 (t-90) cc_final: 0.0329 (t-90) REVERT: N 237 MET cc_start: 0.7964 (mmm) cc_final: 0.7613 (mmm) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.1299 time to fit residues: 36.8083 Evaluate side-chains 131 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 20.0000 chunk 84 optimal weight: 30.0000 chunk 165 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 175 optimal weight: 50.0000 chunk 169 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 33 optimal weight: 0.3980 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 100 GLN L 168 HIS L 239 ASN M 193 HIS M 214 HIS N 168 HIS N 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.073782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.038065 restraints weight = 133616.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.038372 restraints weight = 65292.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.038644 restraints weight = 40748.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038934 restraints weight = 31066.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.039016 restraints weight = 26649.923| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.214 19616 Z= 0.277 Angle : 0.788 8.406 27840 Z= 0.434 Chirality : 0.049 0.226 3119 Planarity : 0.006 0.076 2501 Dihedral : 29.706 164.883 5115 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % 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: 1.07 (0.20), residues: 1530 helix: 1.10 (0.19), residues: 615 sheet: 0.78 (0.29), residues: 300 loop : 0.45 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 175 TYR 0.026 0.002 TYR B 51 PHE 0.036 0.002 PHE A 67 TRP 0.011 0.002 TRP K 146 HIS 0.029 0.003 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (19616) covalent geometry : angle 0.78819 / 0.43 (27840) hydrogen bonds : bond 0.08508 / 5.85 ( 1015) hydrogen bonds : angle 4.61688 / 3.38 ( 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 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.551 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: 0.9563 (mm-30) cc_final: 0.9313 (mm-30) REVERT: A 51 ILE cc_start: 0.9700 (mt) cc_final: 0.9496 (mm) REVERT: A 90 MET cc_start: 0.9607 (mmm) cc_final: 0.9381 (mmp) REVERT: A 105 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9230 (tm-30) REVERT: A 106 ASP cc_start: 0.8835 (m-30) cc_final: 0.8348 (m-30) REVERT: B 66 ILE cc_start: 0.9619 (tt) cc_final: 0.9395 (pt) REVERT: B 68 ASP cc_start: 0.9119 (m-30) cc_final: 0.8880 (m-30) REVERT: B 84 MET cc_start: 0.9408 (tpt) cc_final: 0.8995 (tpp) REVERT: C 90 ASP cc_start: 0.9015 (t0) cc_final: 0.8710 (t0) REVERT: D 68 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9153 (mm-30) REVERT: F 68 ASP cc_start: 0.9593 (m-30) cc_final: 0.9181 (m-30) REVERT: F 84 MET cc_start: 0.9537 (tpp) cc_final: 0.9164 (tpp) REVERT: G 64 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8837 (tm-30) REVERT: G 75 LYS cc_start: 0.8783 (mmpt) cc_final: 0.8468 (mmmt) REVERT: G 90 ASP cc_start: 0.8703 (t70) cc_final: 0.8481 (t70) REVERT: H 59 MET cc_start: 0.9741 (tpp) cc_final: 0.9416 (mmp) REVERT: H 97 LEU cc_start: 0.9662 (mt) cc_final: 0.9350 (mt) REVERT: K 246 MET cc_start: -0.0471 (mtt) cc_final: -0.0844 (mtm) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.1401 time to fit residues: 30.0715 Evaluate side-chains 106 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 130 optimal weight: 0.0010 chunk 97 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 26 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 overall best weight: 4.0030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN M 178 HIS M 239 ASN N 168 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.074283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037834 restraints weight = 131811.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.038338 restraints weight = 64579.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038436 restraints weight = 40489.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038585 restraints weight = 31120.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038793 restraints weight = 27159.984| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 19616 Z= 0.186 Angle : 0.638 8.627 27840 Z= 0.363 Chirality : 0.046 0.231 3119 Planarity : 0.005 0.077 2501 Dihedral : 29.731 167.772 5115 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 1.36 (0.21), residues: 1530 helix: 1.52 (0.20), residues: 618 sheet: 0.86 (0.29), residues: 304 loop : 0.43 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 196 TYR 0.025 0.002 TYR F 88 PHE 0.023 0.002 PHE E 104 TRP 0.006 0.001 TRP L 146 HIS 0.010 0.001 HIS K 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (19616) covalent geometry : angle 0.63814 / 0.36 (27840) hydrogen bonds : bond 0.05228 / 3.60 ( 1015) hydrogen bonds : angle 4.09746 / 3.03 ( 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 144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.454 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: 0.9580 (mm-30) cc_final: 0.9312 (mm-30) REVERT: A 51 ILE cc_start: 0.9675 (mt) cc_final: 0.9469 (mm) REVERT: A 90 MET cc_start: 0.9656 (mmm) cc_final: 0.9399 (mmm) REVERT: A 97 GLU cc_start: 0.9109 (pp20) cc_final: 0.8748 (pp20) REVERT: A 105 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9236 (tm-30) REVERT: A 106 ASP cc_start: 0.8929 (m-30) cc_final: 0.8494 (m-30) REVERT: A 120 MET cc_start: 0.9042 (mmp) cc_final: 0.8667 (mmm) REVERT: B 63 GLU cc_start: 0.9159 (pp20) cc_final: 0.8817 (pp20) REVERT: B 84 MET cc_start: 0.9435 (tpt) cc_final: 0.8975 (mmm) REVERT: C 90 ASP cc_start: 0.9130 (t0) cc_final: 0.8705 (t0) REVERT: E 105 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8830 (pp20) REVERT: E 106 ASP cc_start: 0.9147 (m-30) cc_final: 0.8479 (m-30) REVERT: E 119 ILE cc_start: 0.9743 (pt) cc_final: 0.9532 (pt) REVERT: E 120 MET cc_start: 0.8893 (mmp) cc_final: 0.8619 (mmm) REVERT: F 84 MET cc_start: 0.9406 (tpp) cc_final: 0.9169 (tpp) REVERT: G 64 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8900 (tm-30) REVERT: G 75 LYS cc_start: 0.8747 (mmpt) cc_final: 0.8399 (mmmm) REVERT: G 90 ASP cc_start: 0.8522 (t70) cc_final: 0.8305 (t70) REVERT: H 59 MET cc_start: 0.9745 (tpp) cc_final: 0.9496 (mmm) REVERT: N 237 MET cc_start: 0.8031 (mmm) cc_final: 0.7756 (mmm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1421 time to fit residues: 30.6770 Evaluate side-chains 106 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 6.9990 chunk 160 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 154 optimal weight: 50.0000 chunk 125 optimal weight: 50.0000 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 31 HIS G 68 ASN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.073692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036861 restraints weight = 133315.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.037306 restraints weight = 65650.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.037460 restraints weight = 41499.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037590 restraints weight = 31793.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.037535 restraints weight = 26597.555| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 19616 Z= 0.183 Angle : 0.642 8.828 27840 Z= 0.364 Chirality : 0.045 0.247 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.685 169.657 5115 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.41 (0.21), residues: 1530 helix: 1.62 (0.20), residues: 618 sheet: 0.85 (0.29), residues: 304 loop : 0.40 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 134 TYR 0.018 0.001 TYR B 51 PHE 0.022 0.002 PHE A 104 TRP 0.006 0.001 TRP L 146 HIS 0.026 0.002 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (19616) covalent geometry : angle 0.64237 / 0.36 (27840) hydrogen bonds : bond 0.05418 / 3.73 ( 1015) hydrogen bonds : angle 4.09466 / 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 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.552 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: 0.9571 (mm-30) cc_final: 0.9288 (mm-30) REVERT: A 51 ILE cc_start: 0.9695 (mt) cc_final: 0.9491 (mm) REVERT: A 90 MET cc_start: 0.9623 (mmm) cc_final: 0.9366 (mmm) REVERT: A 97 GLU cc_start: 0.9085 (pp20) cc_final: 0.8731 (pp20) REVERT: A 105 GLU cc_start: 0.9472 (tm-30) cc_final: 0.9244 (tm-30) REVERT: A 106 ASP cc_start: 0.8891 (m-30) cc_final: 0.8443 (m-30) REVERT: A 120 MET cc_start: 0.9106 (mmp) cc_final: 0.8777 (mmm) REVERT: B 37 LEU cc_start: 0.9712 (mm) cc_final: 0.9494 (tt) REVERT: B 43 VAL cc_start: 0.9691 (t) cc_final: 0.9462 (t) REVERT: B 63 GLU cc_start: 0.9171 (pp20) cc_final: 0.8845 (pp20) REVERT: B 68 ASP cc_start: 0.9218 (m-30) cc_final: 0.8998 (m-30) REVERT: B 84 MET cc_start: 0.9424 (tpt) cc_final: 0.8990 (mmm) REVERT: C 90 ASP cc_start: 0.9176 (t0) cc_final: 0.8801 (t70) REVERT: E 92 LEU cc_start: 0.9604 (mt) cc_final: 0.9208 (tp) REVERT: E 96 CYS cc_start: 0.9396 (m) cc_final: 0.8938 (m) REVERT: E 105 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8979 (tm-30) REVERT: E 106 ASP cc_start: 0.9161 (m-30) cc_final: 0.8504 (m-30) REVERT: E 120 MET cc_start: 0.9020 (mmp) cc_final: 0.8819 (mmm) REVERT: F 63 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9260 (mp0) REVERT: G 64 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8865 (tm-30) REVERT: G 68 ASN cc_start: 0.8999 (m-40) cc_final: 0.8642 (m110) REVERT: G 75 LYS cc_start: 0.8954 (mmpt) cc_final: 0.8629 (mmmm) REVERT: G 90 ASP cc_start: 0.8527 (t70) cc_final: 0.8315 (t70) REVERT: H 59 MET cc_start: 0.9710 (tpp) cc_final: 0.9457 (mmm) REVERT: K 169 MET cc_start: -0.0625 (tpt) cc_final: -0.0841 (tpt) REVERT: K 236 TYR cc_start: 0.5344 (m-80) cc_final: 0.5125 (m-80) REVERT: K 246 MET cc_start: -0.0235 (mtt) cc_final: -0.0453 (mtm) REVERT: N 237 MET cc_start: 0.8000 (mmm) cc_final: 0.7746 (mmm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1193 time to fit residues: 26.8679 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 : 0.550 ------------------------------------------------------------------------------- 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: 40.0000 chunk 145 optimal weight: 5.9990 chunk 169 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 168 optimal weight: 40.0000 chunk 105 optimal weight: 40.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.073411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.036121 restraints weight = 133685.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036602 restraints weight = 64606.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036781 restraints weight = 40442.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036890 restraints weight = 31693.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037034 restraints weight = 27369.814| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 19616 Z= 0.167 Angle : 0.629 9.472 27840 Z= 0.356 Chirality : 0.045 0.261 3119 Planarity : 0.005 0.070 2501 Dihedral : 29.679 173.611 5115 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.21), residues: 1530 helix: 1.70 (0.20), residues: 617 sheet: 0.88 (0.30), residues: 300 loop : 0.44 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 196 TYR 0.041 0.001 TYR H 80 PHE 0.029 0.002 PHE E 104 TRP 0.006 0.001 TRP K 146 HIS 0.017 0.001 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (19616) covalent geometry : angle 0.62881 / 0.36 (27840) hydrogen bonds : bond 0.04794 / 3.32 ( 1015) hydrogen bonds : angle 3.97322 / 2.93 ( 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 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.552 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: 0.9597 (mm-30) cc_final: 0.9308 (mm-30) REVERT: A 51 ILE cc_start: 0.9621 (mt) cc_final: 0.9400 (mm) REVERT: A 84 PHE cc_start: 0.9263 (m-80) cc_final: 0.8996 (m-80) REVERT: A 90 MET cc_start: 0.9641 (mmm) cc_final: 0.9426 (mmp) REVERT: A 97 GLU cc_start: 0.9153 (pp20) cc_final: 0.8781 (pp20) REVERT: A 105 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9254 (tm-30) REVERT: A 106 ASP cc_start: 0.8925 (m-30) cc_final: 0.8514 (m-30) REVERT: A 120 MET cc_start: 0.9087 (mmp) cc_final: 0.8643 (mmm) REVERT: B 37 LEU cc_start: 0.9744 (mm) cc_final: 0.9477 (tt) REVERT: B 63 GLU cc_start: 0.9186 (pp20) cc_final: 0.8887 (pp20) REVERT: B 66 ILE cc_start: 0.9628 (tt) cc_final: 0.9380 (pt) REVERT: B 68 ASP cc_start: 0.9303 (m-30) cc_final: 0.9061 (m-30) REVERT: B 84 MET cc_start: 0.9451 (tpt) cc_final: 0.9231 (mmm) REVERT: C 90 ASP cc_start: 0.9122 (t0) cc_final: 0.8729 (t70) REVERT: E 92 LEU cc_start: 0.9587 (mt) cc_final: 0.9236 (tp) REVERT: E 96 CYS cc_start: 0.9382 (m) cc_final: 0.8947 (m) REVERT: E 106 ASP cc_start: 0.9168 (m-30) cc_final: 0.8613 (m-30) REVERT: G 64 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8921 (tm-30) REVERT: G 68 ASN cc_start: 0.9095 (m-40) cc_final: 0.8745 (m110) REVERT: G 75 LYS cc_start: 0.8906 (mmpt) cc_final: 0.8596 (mmmm) REVERT: G 90 ASP cc_start: 0.8415 (t70) cc_final: 0.8188 (t0) REVERT: H 59 MET cc_start: 0.9753 (tpp) cc_final: 0.9496 (mmm) REVERT: K 236 TYR cc_start: 0.5354 (m-80) cc_final: 0.5122 (m-80) REVERT: K 246 MET cc_start: -0.0052 (mtt) cc_final: -0.0435 (mtm) REVERT: N 133 MET cc_start: 0.6744 (ppp) cc_final: 0.6414 (ppp) REVERT: N 237 MET cc_start: 0.8009 (mmm) cc_final: 0.7796 (mmm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1223 time to fit residues: 27.7694 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 : 0.479 ------------------------------------------------------------------------------- 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: 1.9990 chunk 133 optimal weight: 50.0000 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 144 optimal weight: 50.0000 chunk 154 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.074344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037019 restraints weight = 130732.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037595 restraints weight = 60355.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.037858 restraints weight = 38086.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038091 restraints weight = 30183.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.038260 restraints weight = 25650.885| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5009 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= 0.127 Angle : 0.600 8.525 27840 Z= 0.340 Chirality : 0.044 0.272 3119 Planarity : 0.004 0.052 2501 Dihedral : 29.607 175.665 5115 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 1.57 (0.21), residues: 1530 helix: 1.81 (0.20), residues: 619 sheet: 0.85 (0.29), residues: 304 loop : 0.46 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 39 TYR 0.029 0.001 TYR H 80 PHE 0.020 0.001 PHE E 104 TRP 0.006 0.001 TRP K 146 HIS 0.020 0.001 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (19616) covalent geometry : angle 0.59961 / 0.34 (27840) hydrogen bonds : bond 0.04280 / 2.97 ( 1015) hydrogen bonds : angle 3.77929 / 2.78 ( 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 150 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.536 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: 0.9627 (mm-30) cc_final: 0.9295 (mm-30) REVERT: A 51 ILE cc_start: 0.9503 (mt) cc_final: 0.9293 (mm) REVERT: A 93 GLN cc_start: 0.9351 (tt0) cc_final: 0.9025 (tp40) REVERT: A 97 GLU cc_start: 0.9195 (pp20) cc_final: 0.8811 (pp20) REVERT: A 105 GLU cc_start: 0.9525 (tm-30) cc_final: 0.9304 (tm-30) REVERT: A 106 ASP cc_start: 0.9011 (m-30) cc_final: 0.8496 (m-30) REVERT: A 120 MET cc_start: 0.8940 (mmp) cc_final: 0.8460 (mmm) REVERT: B 63 GLU cc_start: 0.9197 (pp20) cc_final: 0.8919 (pp20) REVERT: B 68 ASP cc_start: 0.9369 (m-30) cc_final: 0.9134 (m-30) REVERT: B 84 MET cc_start: 0.9380 (tpt) cc_final: 0.9143 (mmm) REVERT: C 90 ASP cc_start: 0.8939 (t0) cc_final: 0.8540 (t70) REVERT: D 59 MET cc_start: 0.9702 (mmm) cc_final: 0.9291 (mmm) REVERT: E 92 LEU cc_start: 0.9562 (mt) cc_final: 0.9342 (tp) REVERT: E 97 GLU cc_start: 0.9074 (pm20) cc_final: 0.8872 (pm20) REVERT: E 106 ASP cc_start: 0.8953 (m-30) cc_final: 0.8617 (m-30) REVERT: E 123 ASP cc_start: 0.8527 (m-30) cc_final: 0.8293 (m-30) REVERT: F 79 LYS cc_start: 0.9450 (mtmm) cc_final: 0.9197 (mtmm) REVERT: G 64 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8974 (tm-30) REVERT: G 68 ASN cc_start: 0.9100 (m-40) cc_final: 0.8772 (m110) REVERT: G 75 LYS cc_start: 0.8839 (mmpt) cc_final: 0.8560 (mmmm) REVERT: G 90 ASP cc_start: 0.8253 (t70) cc_final: 0.8044 (t0) REVERT: H 59 MET cc_start: 0.9810 (tpp) cc_final: 0.9258 (mmm) REVERT: K 193 HIS cc_start: 0.1913 (t-90) cc_final: 0.1500 (t-90) REVERT: L 243 MET cc_start: 0.0111 (ppp) cc_final: -0.0102 (ppp) REVERT: N 133 MET cc_start: 0.6750 (ppp) cc_final: 0.6452 (ppp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1241 time to fit residues: 28.8582 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 : 0.462 ------------------------------------------------------------------------------- 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: 0.0570 chunk 96 optimal weight: 30.0000 chunk 109 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 147 optimal weight: 50.0000 chunk 145 optimal weight: 0.0030 chunk 153 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 2.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.073604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036957 restraints weight = 131114.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037260 restraints weight = 61253.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037716 restraints weight = 41065.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037720 restraints weight = 30072.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037847 restraints weight = 25354.235| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19616 Z= 0.140 Angle : 0.607 10.066 27840 Z= 0.344 Chirality : 0.044 0.275 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.565 177.679 5115 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.21), residues: 1530 helix: 1.71 (0.20), residues: 618 sheet: 0.84 (0.29), residues: 304 loop : 0.42 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 196 TYR 0.032 0.001 TYR H 80 PHE 0.016 0.001 PHE E 104 TRP 0.005 0.001 TRP K 146 HIS 0.019 0.001 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (19616) covalent geometry : angle 0.60726 / 0.34 (27840) hydrogen bonds : bond 0.04459 / 3.09 ( 1015) hydrogen bonds : angle 3.83881 / 2.83 ( 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 : 0.551 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: 0.9646 (mm-30) cc_final: 0.9345 (mm-30) REVERT: A 97 GLU cc_start: 0.9205 (pp20) cc_final: 0.8816 (pp20) REVERT: A 105 GLU cc_start: 0.9553 (tm-30) cc_final: 0.9326 (tm-30) REVERT: A 106 ASP cc_start: 0.8913 (m-30) cc_final: 0.8464 (m-30) REVERT: A 120 MET cc_start: 0.8927 (mmp) cc_final: 0.8448 (mmm) REVERT: B 63 GLU cc_start: 0.9266 (pp20) cc_final: 0.9031 (pp20) REVERT: B 66 ILE cc_start: 0.9611 (tt) cc_final: 0.9378 (pt) REVERT: B 68 ASP cc_start: 0.9405 (m-30) cc_final: 0.9170 (m-30) REVERT: B 84 MET cc_start: 0.9419 (tpt) cc_final: 0.9168 (mmm) REVERT: C 90 ASP cc_start: 0.8862 (t0) cc_final: 0.8470 (t70) REVERT: D 59 MET cc_start: 0.9706 (mmm) cc_final: 0.9309 (mmm) REVERT: D 97 LEU cc_start: 0.9652 (mt) cc_final: 0.9405 (mt) REVERT: E 92 LEU cc_start: 0.9558 (mt) cc_final: 0.9329 (tp) REVERT: E 106 ASP cc_start: 0.8841 (m-30) cc_final: 0.8587 (m-30) REVERT: F 79 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9110 (mtmm) REVERT: G 64 GLU cc_start: 0.9290 (tm-30) cc_final: 0.9014 (tm-30) REVERT: G 68 ASN cc_start: 0.9130 (m-40) cc_final: 0.8814 (m110) REVERT: G 75 LYS cc_start: 0.8897 (mmpt) cc_final: 0.8640 (mmmm) REVERT: G 90 ASP cc_start: 0.8196 (t70) cc_final: 0.7961 (t0) REVERT: H 59 MET cc_start: 0.9821 (tpp) cc_final: 0.9291 (mmm) REVERT: K 193 HIS cc_start: 0.1915 (t-90) cc_final: 0.1490 (t-90) REVERT: L 243 MET cc_start: 0.0438 (ppp) cc_final: 0.0228 (ppp) REVERT: N 133 MET cc_start: 0.6762 (ppp) cc_final: 0.6480 (ppp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1311 time to fit residues: 29.6318 Evaluate side-chains 116 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 30.0000 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN M 100 GLN N 168 HIS N 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.072470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.035950 restraints weight = 132159.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036284 restraints weight = 62369.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036720 restraints weight = 41283.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036875 restraints weight = 31172.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037160 restraints weight = 27528.838| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 19616 Z= 0.175 Angle : 0.635 11.674 27840 Z= 0.356 Chirality : 0.044 0.278 3119 Planarity : 0.004 0.054 2501 Dihedral : 29.650 179.173 5115 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.44 (0.21), residues: 1530 helix: 1.65 (0.20), residues: 624 sheet: 0.83 (0.29), residues: 300 loop : 0.43 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.031 0.001 TYR H 80 PHE 0.017 0.001 PHE E 104 TRP 0.005 0.001 TRP K 146 HIS 0.017 0.001 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (19616) covalent geometry : angle 0.63535 / 0.36 (27840) hydrogen bonds : bond 0.05048 / 3.48 ( 1015) hydrogen bonds : angle 3.89465 / 2.86 ( 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 136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.521 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: 0.9630 (mm-30) cc_final: 0.9400 (mm-30) REVERT: A 52 ARG cc_start: 0.9238 (mtt90) cc_final: 0.8922 (mtm-85) REVERT: A 84 PHE cc_start: 0.8982 (m-80) cc_final: 0.8464 (m-80) REVERT: A 97 GLU cc_start: 0.9201 (pp20) cc_final: 0.8827 (pp20) REVERT: A 105 GLU cc_start: 0.9548 (tm-30) cc_final: 0.9328 (tm-30) REVERT: A 106 ASP cc_start: 0.8890 (m-30) cc_final: 0.8414 (m-30) REVERT: A 120 MET cc_start: 0.9038 (mmp) cc_final: 0.8543 (mmm) REVERT: B 63 GLU cc_start: 0.9242 (pp20) cc_final: 0.9023 (pp20) REVERT: B 66 ILE cc_start: 0.9628 (tt) cc_final: 0.9403 (pt) REVERT: B 68 ASP cc_start: 0.9394 (m-30) cc_final: 0.9171 (m-30) REVERT: B 84 MET cc_start: 0.9497 (tpt) cc_final: 0.9231 (mmm) REVERT: C 90 ASP cc_start: 0.9008 (t0) cc_final: 0.8613 (t70) REVERT: D 97 LEU cc_start: 0.9653 (mt) cc_final: 0.9368 (mt) REVERT: E 92 LEU cc_start: 0.9557 (mt) cc_final: 0.9299 (tt) REVERT: E 106 ASP cc_start: 0.8846 (m-30) cc_final: 0.8607 (m-30) REVERT: F 79 LYS cc_start: 0.9409 (mtmm) cc_final: 0.8854 (ptpp) REVERT: F 84 MET cc_start: 0.9575 (mmp) cc_final: 0.9314 (tpp) REVERT: G 64 GLU cc_start: 0.9281 (tm-30) cc_final: 0.8981 (tm-30) REVERT: G 68 ASN cc_start: 0.9101 (m-40) cc_final: 0.8798 (m110) REVERT: G 75 LYS cc_start: 0.8965 (mmpt) cc_final: 0.8681 (mmmm) REVERT: G 90 ASP cc_start: 0.8337 (t70) cc_final: 0.8127 (t0) REVERT: H 59 MET cc_start: 0.9807 (tpp) cc_final: 0.9288 (mmm) REVERT: K 193 HIS cc_start: 0.1928 (t-90) cc_final: 0.1423 (t-90) REVERT: K 236 TYR cc_start: 0.5383 (m-80) cc_final: 0.5152 (m-80) REVERT: L 243 MET cc_start: 0.0329 (ppp) cc_final: 0.0120 (ppp) REVERT: N 133 MET cc_start: 0.6755 (ppp) cc_final: 0.6488 (ppp) REVERT: N 237 MET cc_start: 0.8103 (mmm) cc_final: 0.7852 (mmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1337 time to fit residues: 28.2296 Evaluate side-chains 111 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 3.9990 chunk 147 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.074003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.037099 restraints weight = 132540.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037459 restraints weight = 61694.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038015 restraints weight = 40792.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038112 restraints weight = 30098.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.038244 restraints weight = 25910.436| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19616 Z= 0.124 Angle : 0.602 10.499 27840 Z= 0.340 Chirality : 0.044 0.283 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.580 177.598 5115 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 1.47 (0.21), residues: 1530 helix: 1.69 (0.20), residues: 623 sheet: 0.80 (0.30), residues: 300 loop : 0.45 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 248 TYR 0.029 0.001 TYR H 80 PHE 0.012 0.001 PHE F 61 TRP 0.005 0.001 TRP K 146 HIS 0.016 0.001 HIS M 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (19616) covalent geometry : angle 0.60243 / 0.34 (27840) hydrogen bonds : bond 0.04123 / 2.86 ( 1015) hydrogen bonds : angle 3.74686 / 2.75 ( 2529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4791.78 seconds wall clock time: 82 minutes 49.67 seconds (4969.67 seconds total)