Starting phenix.real_space_refine on Mon Jun 16 06:07:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzz_33535/06_2025/7xzz_33535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzz_33535/06_2025/7xzz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xzz_33535/06_2025/7xzz_33535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzz_33535/06_2025/7xzz_33535.map" model { file = "/net/cci-nas-00/data/ceres_data/7xzz_33535/06_2025/7xzz_33535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzz_33535/06_2025/7xzz_33535_neut.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.92, per 1000 atoms: 0.59 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: 4.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 7.85 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: 7.44 Time building geometry restraints manager: 5.23 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=" 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=" 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 bond pdb=" N VAL K 122 " pdb=" CA VAL K 122 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N VAL N 225 " pdb=" CA VAL N 225 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.24e-02 6.50e+03 1.06e+01 ... (remaining 19611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 25847 1.73 - 3.45: 1783 3.45 - 5.18: 182 5.18 - 6.91: 25 6.91 - 8.63: 3 Bond angle restraints: 27840 Sorted by residual: angle pdb=" O PRO L 190 " pdb=" C PRO L 190 " pdb=" N PRO L 191 " ideal model delta sigma weight residual 121.31 123.33 -2.02 4.60e-01 4.73e+00 1.94e+01 angle pdb=" N LEU M 265 " pdb=" CA LEU M 265 " pdb=" C LEU M 265 " ideal model delta sigma weight residual 113.88 108.67 5.21 1.23e+00 6.61e-01 1.79e+01 angle pdb=" O PRO M 190 " pdb=" C PRO M 190 " pdb=" N PRO M 191 " ideal model delta sigma weight residual 121.31 123.17 -1.86 4.60e-01 4.73e+00 1.64e+01 angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta sigma weight residual 110.32 117.15 -6.83 1.70e+00 3.46e-01 1.61e+01 angle pdb=" O3' DG I 130 " pdb=" C3' DG I 130 " pdb=" C2' DG I 130 " ideal model delta sigma weight residual 111.50 105.57 5.93 1.50e+00 4.44e-01 1.56e+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: 2240 0.052 - 0.103: 618 0.103 - 0.155: 175 0.155 - 0.206: 78 0.206 - 0.258: 8 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 47.410 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4393 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 19616 Z= 0.342 Angle : 0.915 8.632 27840 Z= 0.608 Chirality : 0.057 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.002 TRP N 146 HIS 0.010 0.002 HIS K 233 PHE 0.018 0.002 PHE N 270 TYR 0.026 0.003 TYR B 88 ARG 0.007 0.001 ARG M 267 Details of bonding type rmsd hydrogen bonds : bond 0.11363 ( 1015) hydrogen bonds : angle 5.24993 ( 2529) covalent geometry : bond 0.00582 (19616) covalent geometry : angle 0.91516 (27840) *********************** 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 : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.3179 time to fit residues: 123.0203 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 : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 50.0000 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS K 178 HIS K 268 ASN K 288 ASN L 168 HIS 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.076174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.040881 restraints weight = 130463.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041557 restraints weight = 61111.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.041695 restraints weight = 38600.662| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.160 19616 Z= 0.312 Angle : 0.737 8.517 27840 Z= 0.419 Chirality : 0.044 0.252 3119 Planarity : 0.006 0.064 2501 Dihedral : 29.087 158.705 5115 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.22 % Allowed : 4.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1530 helix: 1.29 (0.19), residues: 620 sheet: 0.54 (0.28), residues: 308 loop : 0.48 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 146 HIS 0.012 0.002 HIS A 113 PHE 0.027 0.002 PHE E 67 TYR 0.018 0.002 TYR A 99 ARG 0.010 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.07852 ( 1015) hydrogen bonds : angle 4.47046 ( 2529) covalent geometry : bond 0.00687 (19616) covalent geometry : angle 0.73738 (27840) *********************** 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 170 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.9079 (mtt90) cc_final: 0.8874 (ptp-170) REVERT: A 90 MET cc_start: 0.9690 (mmm) cc_final: 0.9431 (mmm) REVERT: A 105 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9287 (tm-30) REVERT: A 106 ASP cc_start: 0.8998 (m-30) cc_final: 0.8527 (m-30) REVERT: B 68 ASP cc_start: 0.9243 (m-30) cc_final: 0.8903 (m-30) REVERT: B 84 MET cc_start: 0.9326 (tpp) cc_final: 0.9122 (mmm) REVERT: C 90 ASP cc_start: 0.8750 (t0) cc_final: 0.8448 (t0) REVERT: D 110 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8552 (mt-10) REVERT: E 94 GLU cc_start: 0.9337 (tp30) cc_final: 0.8836 (tp30) REVERT: E 106 ASP cc_start: 0.8822 (m-30) cc_final: 0.8567 (m-30) REVERT: F 63 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9190 (mp0) REVERT: G 38 ASN cc_start: 0.9056 (m-40) cc_final: 0.8158 (t0) REVERT: G 64 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8903 (tm-30) REVERT: G 90 ASP cc_start: 0.8416 (t70) cc_final: 0.8146 (t0) REVERT: H 59 MET cc_start: 0.9838 (tpp) cc_final: 0.9477 (mmp) REVERT: K 246 MET cc_start: -0.0055 (mtt) cc_final: -0.0579 (mtm) REVERT: N 237 MET cc_start: 0.8031 (mmm) cc_final: 0.7621 (mmm) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.3272 time to fit residues: 81.6675 Evaluate side-chains 120 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 135 optimal weight: 50.0000 chunk 133 optimal weight: 8.9990 chunk 158 optimal weight: 30.0000 chunk 126 optimal weight: 0.0270 chunk 157 optimal weight: 50.0000 chunk 33 optimal weight: 0.9990 chunk 175 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 overall best weight: 8.6048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 68 GLN H 46 HIS K 100 GLN K 239 ASN M 193 HIS M 214 HIS ** M 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 214 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.069865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.034456 restraints weight = 137082.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.034819 restraints weight = 71466.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.034941 restraints weight = 46334.048| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.137 19616 Z= 0.419 Angle : 0.822 13.790 27840 Z= 0.463 Chirality : 0.047 0.306 3119 Planarity : 0.006 0.072 2501 Dihedral : 29.684 165.675 5115 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.22 % Allowed : 5.72 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1530 helix: 0.62 (0.19), residues: 621 sheet: 0.61 (0.28), residues: 304 loop : 0.26 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 146 HIS 0.015 0.002 HIS A 113 PHE 0.038 0.002 PHE E 67 TYR 0.028 0.003 TYR H 37 ARG 0.009 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.08412 ( 1015) hydrogen bonds : angle 5.00712 ( 2529) covalent geometry : bond 0.00908 (19616) covalent geometry : angle 0.82240 (27840) *********************** 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 147 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.709 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: 0.9592 (mm-30) cc_final: 0.9284 (mm-30) REVERT: A 77 ASP cc_start: 0.9555 (m-30) cc_final: 0.9272 (p0) REVERT: A 93 GLN cc_start: 0.9501 (tt0) cc_final: 0.9180 (tp40) REVERT: A 96 CYS cc_start: 0.9492 (m) cc_final: 0.9232 (m) REVERT: A 106 ASP cc_start: 0.8938 (m-30) cc_final: 0.8483 (m-30) REVERT: B 68 ASP cc_start: 0.9305 (m-30) cc_final: 0.9104 (m-30) REVERT: B 74 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9189 (tm-30) REVERT: B 84 MET cc_start: 0.9494 (tpp) cc_final: 0.9048 (mmm) REVERT: C 90 ASP cc_start: 0.9152 (t0) cc_final: 0.8837 (t0) REVERT: E 92 LEU cc_start: 0.9573 (tp) cc_final: 0.9275 (tt) REVERT: E 96 CYS cc_start: 0.9390 (m) cc_final: 0.9010 (m) REVERT: E 103 LEU cc_start: 0.9719 (tt) cc_final: 0.9419 (mm) REVERT: E 106 ASP cc_start: 0.8887 (m-30) cc_final: 0.8597 (m-30) REVERT: E 123 ASP cc_start: 0.8861 (m-30) cc_final: 0.8597 (m-30) REVERT: F 79 LYS cc_start: 0.9274 (mppt) cc_final: 0.9009 (mttt) REVERT: G 75 LYS cc_start: 0.8883 (mmpt) cc_final: 0.8591 (mmmt) REVERT: G 90 ASP cc_start: 0.8861 (t70) cc_final: 0.8553 (t70) REVERT: H 59 MET cc_start: 0.9803 (tpp) cc_final: 0.9540 (mmp) REVERT: H 97 LEU cc_start: 0.9722 (mt) cc_final: 0.9474 (mt) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.3245 time to fit residues: 71.0533 Evaluate side-chains 102 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 137 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 174 optimal weight: 50.0000 chunk 108 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 60 ASN E 93 GLN H 46 HIS ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 HIS K 235 ASN M 239 ASN N 168 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.071977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035045 restraints weight = 135092.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035413 restraints weight = 67946.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.035574 restraints weight = 42940.980| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 19616 Z= 0.225 Angle : 0.630 10.681 27840 Z= 0.364 Chirality : 0.040 0.168 3119 Planarity : 0.004 0.049 2501 Dihedral : 29.726 169.047 5115 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1530 helix: 1.26 (0.19), residues: 620 sheet: 0.80 (0.29), residues: 304 loop : 0.33 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 146 HIS 0.013 0.001 HIS F 75 PHE 0.019 0.002 PHE A 104 TYR 0.015 0.001 TYR D 37 ARG 0.011 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 1015) hydrogen bonds : angle 4.14128 ( 2529) covalent geometry : bond 0.00490 (19616) covalent geometry : angle 0.62997 (27840) *********************** 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 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9331 (mm-30) REVERT: A 93 GLN cc_start: 0.9501 (tt0) cc_final: 0.9285 (tp40) REVERT: A 106 ASP cc_start: 0.9130 (m-30) cc_final: 0.8655 (m-30) REVERT: A 119 ILE cc_start: 0.9609 (pt) cc_final: 0.9329 (mm) REVERT: A 120 MET cc_start: 0.8979 (mmp) cc_final: 0.8489 (mmm) REVERT: B 43 VAL cc_start: 0.9661 (t) cc_final: 0.9428 (t) REVERT: B 63 GLU cc_start: 0.9200 (pp20) cc_final: 0.8985 (pp20) REVERT: B 66 ILE cc_start: 0.9823 (mm) cc_final: 0.9590 (tt) REVERT: B 74 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9160 (tm-30) REVERT: C 90 ASP cc_start: 0.9050 (t0) cc_final: 0.8703 (t0) REVERT: E 92 LEU cc_start: 0.9511 (tp) cc_final: 0.9206 (tt) REVERT: E 96 CYS cc_start: 0.9402 (m) cc_final: 0.9059 (m) REVERT: E 103 LEU cc_start: 0.9744 (tt) cc_final: 0.9512 (mm) REVERT: E 106 ASP cc_start: 0.8936 (m-30) cc_final: 0.8701 (m-30) REVERT: F 63 GLU cc_start: 0.9548 (mt-10) cc_final: 0.9257 (mt-10) REVERT: G 90 ASP cc_start: 0.8735 (t70) cc_final: 0.8321 (t70) REVERT: K 193 HIS cc_start: 0.2073 (t-90) cc_final: 0.1819 (t-90) REVERT: K 246 MET cc_start: 0.0198 (mtt) cc_final: -0.0134 (mtm) REVERT: N 160 MET cc_start: -0.1987 (tmm) cc_final: -0.2366 (tmm) REVERT: N 237 MET cc_start: 0.8052 (mmm) cc_final: 0.7821 (mmm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3102 time to fit residues: 65.8342 Evaluate side-chains 99 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 57 optimal weight: 0.8980 chunk 129 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 140 optimal weight: 50.0000 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN H 46 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.072868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035435 restraints weight = 133726.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035806 restraints weight = 65482.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.036268 restraints weight = 44045.386| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19616 Z= 0.166 Angle : 0.593 9.385 27840 Z= 0.342 Chirality : 0.039 0.180 3119 Planarity : 0.004 0.052 2501 Dihedral : 29.529 171.360 5115 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1530 helix: 1.60 (0.20), residues: 620 sheet: 0.88 (0.30), residues: 300 loop : 0.45 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.010 0.001 HIS F 75 PHE 0.014 0.001 PHE G 25 TYR 0.017 0.001 TYR F 88 ARG 0.005 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 1015) hydrogen bonds : angle 3.84412 ( 2529) covalent geometry : bond 0.00366 (19616) covalent geometry : angle 0.59301 (27840) *********************** 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 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.599 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: 0.9590 (mm-30) cc_final: 0.9327 (mm-30) REVERT: A 106 ASP cc_start: 0.9124 (m-30) cc_final: 0.8605 (m-30) REVERT: A 120 MET cc_start: 0.8979 (mmp) cc_final: 0.8429 (mmm) REVERT: B 63 GLU cc_start: 0.9175 (pp20) cc_final: 0.8957 (pp20) REVERT: B 66 ILE cc_start: 0.9824 (mm) cc_final: 0.9596 (tt) REVERT: B 68 ASP cc_start: 0.9196 (m-30) cc_final: 0.8984 (m-30) REVERT: B 74 GLU cc_start: 0.9387 (tm-30) cc_final: 0.9143 (tm-30) REVERT: C 90 ASP cc_start: 0.9130 (t0) cc_final: 0.8679 (t0) REVERT: E 92 LEU cc_start: 0.9488 (tp) cc_final: 0.9169 (tt) REVERT: E 96 CYS cc_start: 0.9371 (m) cc_final: 0.8962 (m) REVERT: E 103 LEU cc_start: 0.9746 (tt) cc_final: 0.9539 (mm) REVERT: E 105 GLU cc_start: 0.9283 (tm-30) cc_final: 0.8981 (pp20) REVERT: E 106 ASP cc_start: 0.9267 (m-30) cc_final: 0.8681 (m-30) REVERT: E 119 ILE cc_start: 0.9725 (pt) cc_final: 0.9505 (pt) REVERT: E 120 MET cc_start: 0.8851 (mmp) cc_final: 0.8284 (mmm) REVERT: E 123 ASP cc_start: 0.8772 (m-30) cc_final: 0.8401 (m-30) REVERT: G 68 ASN cc_start: 0.9420 (m-40) cc_final: 0.8886 (m110) REVERT: G 75 LYS cc_start: 0.9009 (mmpt) cc_final: 0.8697 (mmmm) REVERT: K 246 MET cc_start: 0.0187 (mtt) cc_final: -0.0150 (mtm) REVERT: N 160 MET cc_start: -0.1956 (tmm) cc_final: -0.2377 (tmm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2998 time to fit residues: 66.1877 Evaluate side-chains 105 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 94 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 114 optimal weight: 50.0000 chunk 155 optimal weight: 30.0000 chunk 128 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 60 ASN G 68 ASN G 112 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.071282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.034112 restraints weight = 137465.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.034650 restraints weight = 67939.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034780 restraints weight = 44318.698| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 19616 Z= 0.238 Angle : 0.621 11.375 27840 Z= 0.357 Chirality : 0.039 0.174 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.513 175.381 5115 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1530 helix: 1.47 (0.20), residues: 625 sheet: 0.92 (0.29), residues: 300 loop : 0.44 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 146 HIS 0.010 0.001 HIS F 75 PHE 0.022 0.002 PHE E 104 TYR 0.052 0.001 TYR H 80 ARG 0.010 0.000 ARG M 196 Details of bonding type rmsd hydrogen bonds : bond 0.05688 ( 1015) hydrogen bonds : angle 4.06301 ( 2529) covalent geometry : bond 0.00524 (19616) covalent geometry : angle 0.62144 (27840) *********************** 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 131 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9346 (mm-30) REVERT: A 106 ASP cc_start: 0.8843 (m-30) cc_final: 0.8631 (m-30) REVERT: A 120 MET cc_start: 0.9141 (mmp) cc_final: 0.8565 (mmm) REVERT: B 66 ILE cc_start: 0.9837 (mm) cc_final: 0.9590 (tt) REVERT: B 74 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9162 (tm-30) REVERT: B 84 MET cc_start: 0.9210 (tpp) cc_final: 0.8934 (mmm) REVERT: C 90 ASP cc_start: 0.9057 (t0) cc_final: 0.8756 (t0) REVERT: E 92 LEU cc_start: 0.9521 (tp) cc_final: 0.9219 (tt) REVERT: E 96 CYS cc_start: 0.9399 (m) cc_final: 0.9047 (m) REVERT: E 105 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8988 (pp20) REVERT: E 106 ASP cc_start: 0.9266 (m-30) cc_final: 0.8661 (m-30) REVERT: E 120 MET cc_start: 0.8898 (mmp) cc_final: 0.8263 (mmm) REVERT: E 123 ASP cc_start: 0.8760 (m-30) cc_final: 0.8357 (m-30) REVERT: K 236 TYR cc_start: 0.5082 (m-80) cc_final: 0.4820 (m-80) REVERT: K 246 MET cc_start: 0.0178 (mtt) cc_final: -0.0170 (mtm) REVERT: N 133 MET cc_start: 0.6756 (ppp) cc_final: 0.6443 (ppp) REVERT: N 160 MET cc_start: -0.1954 (tmm) cc_final: -0.2369 (tmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2979 time to fit residues: 60.4061 Evaluate side-chains 92 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 138 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 154 optimal weight: 50.0000 chunk 133 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN G 112 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3682 r_free = 0.3682 target = 0.071961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034882 restraints weight = 134348.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035258 restraints weight = 68331.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.035436 restraints weight = 47305.913| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19616 Z= 0.184 Angle : 0.598 10.510 27840 Z= 0.344 Chirality : 0.038 0.197 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.520 178.431 5115 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.21), residues: 1530 helix: 1.69 (0.20), residues: 625 sheet: 0.96 (0.29), residues: 300 loop : 0.42 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 146 HIS 0.009 0.001 HIS F 75 PHE 0.011 0.001 PHE G 25 TYR 0.029 0.001 TYR H 80 ARG 0.011 0.000 ARG L 196 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 1015) hydrogen bonds : angle 3.89146 ( 2529) covalent geometry : bond 0.00402 (19616) covalent geometry : angle 0.59850 (27840) *********************** 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 128 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9348 (mm-30) REVERT: A 120 MET cc_start: 0.8983 (mmp) cc_final: 0.8387 (mmm) REVERT: B 43 VAL cc_start: 0.9566 (t) cc_final: 0.9357 (t) REVERT: B 63 GLU cc_start: 0.9132 (pp20) cc_final: 0.8931 (pp20) REVERT: B 66 ILE cc_start: 0.9847 (mm) cc_final: 0.9630 (tt) REVERT: B 74 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9167 (tm-30) REVERT: B 84 MET cc_start: 0.9200 (tpp) cc_final: 0.8982 (mmm) REVERT: C 90 ASP cc_start: 0.9022 (t0) cc_final: 0.8725 (t0) REVERT: D 65 ASP cc_start: 0.9476 (t0) cc_final: 0.9191 (t0) REVERT: E 92 LEU cc_start: 0.9519 (tp) cc_final: 0.9207 (tt) REVERT: E 96 CYS cc_start: 0.9409 (m) cc_final: 0.8974 (m) REVERT: E 105 GLU cc_start: 0.9300 (tm-30) cc_final: 0.8979 (pp20) REVERT: E 106 ASP cc_start: 0.9259 (m-30) cc_final: 0.8602 (m-30) REVERT: E 119 ILE cc_start: 0.9683 (pt) cc_final: 0.9465 (pt) REVERT: E 120 MET cc_start: 0.8919 (mmp) cc_final: 0.8261 (mmm) REVERT: E 123 ASP cc_start: 0.8704 (m-30) cc_final: 0.8303 (m-30) REVERT: G 68 ASN cc_start: 0.9437 (m-40) cc_final: 0.8958 (m110) REVERT: G 90 ASP cc_start: 0.8503 (t70) cc_final: 0.8278 (t70) REVERT: K 169 MET cc_start: -0.0717 (tpt) cc_final: -0.0942 (tpt) REVERT: K 193 HIS cc_start: 0.1585 (t-90) cc_final: 0.1235 (t70) REVERT: K 236 TYR cc_start: 0.4973 (m-80) cc_final: 0.4740 (m-80) REVERT: K 243 MET cc_start: 0.0950 (ptp) cc_final: 0.0743 (ptp) REVERT: K 246 MET cc_start: 0.0129 (mtt) cc_final: -0.0185 (mtm) REVERT: N 160 MET cc_start: -0.1978 (tmm) cc_final: -0.2371 (tmm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2997 time to fit residues: 59.6641 Evaluate side-chains 97 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 121 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 136 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 160 optimal weight: 0.0970 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN G 112 GLN H 60 ASN ** M 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.072184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034938 restraints weight = 134115.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.035258 restraints weight = 68462.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035579 restraints weight = 46330.025| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19616 Z= 0.168 Angle : 0.586 10.706 27840 Z= 0.336 Chirality : 0.038 0.178 3119 Planarity : 0.004 0.053 2501 Dihedral : 29.403 179.157 5115 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1530 helix: 1.82 (0.20), residues: 625 sheet: 0.93 (0.29), residues: 300 loop : 0.46 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.009 0.001 HIS F 75 PHE 0.013 0.001 PHE E 104 TYR 0.031 0.001 TYR H 80 ARG 0.004 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 1015) hydrogen bonds : angle 3.76452 ( 2529) covalent geometry : bond 0.00371 (19616) covalent geometry : angle 0.58632 (27840) *********************** 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 130 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.541 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: 0.9576 (mm-30) cc_final: 0.9340 (mm-30) REVERT: A 97 GLU cc_start: 0.8961 (pp20) cc_final: 0.8588 (pp20) REVERT: A 106 ASP cc_start: 0.8911 (m-30) cc_final: 0.8567 (m-30) REVERT: A 120 MET cc_start: 0.9000 (mmp) cc_final: 0.8409 (mmm) REVERT: B 43 VAL cc_start: 0.9565 (t) cc_final: 0.9339 (t) REVERT: B 63 GLU cc_start: 0.9146 (pp20) cc_final: 0.8942 (pp20) REVERT: B 66 ILE cc_start: 0.9845 (mm) cc_final: 0.9626 (tt) REVERT: B 68 ASP cc_start: 0.9337 (m-30) cc_final: 0.9132 (m-30) REVERT: B 74 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9134 (tm-30) REVERT: B 84 MET cc_start: 0.9174 (tpp) cc_final: 0.8941 (mmm) REVERT: C 90 ASP cc_start: 0.9005 (t0) cc_final: 0.8721 (t0) REVERT: D 65 ASP cc_start: 0.9445 (t0) cc_final: 0.9140 (t0) REVERT: D 97 LEU cc_start: 0.9678 (mt) cc_final: 0.9372 (mt) REVERT: E 92 LEU cc_start: 0.9519 (tp) cc_final: 0.9216 (tt) REVERT: E 96 CYS cc_start: 0.9354 (m) cc_final: 0.8916 (m) REVERT: E 105 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8956 (pp20) REVERT: E 106 ASP cc_start: 0.9218 (m-30) cc_final: 0.8562 (m-30) REVERT: E 119 ILE cc_start: 0.9680 (pt) cc_final: 0.9447 (pt) REVERT: E 120 MET cc_start: 0.8949 (mmp) cc_final: 0.8269 (mmm) REVERT: E 123 ASP cc_start: 0.8700 (m-30) cc_final: 0.8282 (m-30) REVERT: G 64 GLU cc_start: 0.9325 (pp20) cc_final: 0.9100 (pp20) REVERT: G 68 ASN cc_start: 0.9447 (m-40) cc_final: 0.8969 (m110) REVERT: G 90 ASP cc_start: 0.8519 (t70) cc_final: 0.8275 (t0) REVERT: K 193 HIS cc_start: 0.1569 (t-90) cc_final: 0.1177 (t70) REVERT: K 246 MET cc_start: -0.0019 (mtt) cc_final: -0.0298 (mtm) REVERT: N 133 MET cc_start: 0.6705 (ppp) cc_final: 0.6360 (ppp) REVERT: N 160 MET cc_start: -0.1954 (tmm) cc_final: -0.2335 (tmm) REVERT: N 237 MET cc_start: 0.7921 (mmm) cc_final: 0.7704 (mmm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2933 time to fit residues: 59.2201 Evaluate side-chains 97 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 168 optimal weight: 40.0000 chunk 77 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 165 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN ** M 193 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 = 0.3674 r_free = 0.3674 target = 0.071407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034328 restraints weight = 135800.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.034701 restraints weight = 66686.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035116 restraints weight = 44762.602| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19616 Z= 0.191 Angle : 0.599 11.620 27840 Z= 0.342 Chirality : 0.038 0.160 3119 Planarity : 0.004 0.052 2501 Dihedral : 29.371 177.812 5115 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1530 helix: 1.66 (0.20), residues: 625 sheet: 0.90 (0.29), residues: 300 loop : 0.52 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.009 0.001 HIS K 178 PHE 0.013 0.001 PHE E 104 TYR 0.028 0.001 TYR H 80 ARG 0.007 0.000 ARG M 282 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 1015) hydrogen bonds : angle 3.87681 ( 2529) covalent geometry : bond 0.00420 (19616) covalent geometry : angle 0.59927 (27840) *********************** 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 126 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9594 (mm-30) cc_final: 0.9359 (mm-30) REVERT: A 97 GLU cc_start: 0.9015 (pp20) cc_final: 0.8658 (pp20) REVERT: A 120 MET cc_start: 0.8998 (mmp) cc_final: 0.8428 (mmm) REVERT: B 74 GLU cc_start: 0.9430 (tm-30) cc_final: 0.9170 (tm-30) REVERT: B 84 MET cc_start: 0.9225 (tpp) cc_final: 0.8985 (mmm) REVERT: C 90 ASP cc_start: 0.8989 (t0) cc_final: 0.8707 (t0) REVERT: D 65 ASP cc_start: 0.9450 (t0) cc_final: 0.9142 (t0) REVERT: D 97 LEU cc_start: 0.9669 (mt) cc_final: 0.9367 (mt) REVERT: E 92 LEU cc_start: 0.9540 (tp) cc_final: 0.9225 (tt) REVERT: E 96 CYS cc_start: 0.9374 (m) cc_final: 0.8950 (m) REVERT: E 120 MET cc_start: 0.8965 (mmp) cc_final: 0.8755 (mmm) REVERT: E 123 ASP cc_start: 0.8773 (m-30) cc_final: 0.8502 (m-30) REVERT: F 79 LYS cc_start: 0.9397 (mtmm) cc_final: 0.9065 (mtmm) REVERT: G 64 GLU cc_start: 0.9327 (pp20) cc_final: 0.9097 (pp20) REVERT: G 68 ASN cc_start: 0.9422 (m-40) cc_final: 0.8946 (m110) REVERT: G 75 LYS cc_start: 0.9106 (mmpt) cc_final: 0.8777 (mmmm) REVERT: G 90 ASP cc_start: 0.8512 (t70) cc_final: 0.8273 (t0) REVERT: H 97 LEU cc_start: 0.9643 (mt) cc_final: 0.9282 (tp) REVERT: K 193 HIS cc_start: 0.1560 (t-90) cc_final: 0.1177 (t-90) REVERT: K 236 TYR cc_start: 0.5203 (m-80) cc_final: 0.4926 (m-80) REVERT: K 246 MET cc_start: 0.0022 (mtt) cc_final: -0.0297 (mtm) REVERT: N 133 MET cc_start: 0.6804 (ppp) cc_final: 0.6505 (ppp) REVERT: N 160 MET cc_start: -0.1821 (tmm) cc_final: -0.2189 (tmm) REVERT: N 237 MET cc_start: 0.7937 (mmm) cc_final: 0.7714 (mmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2995 time to fit residues: 59.2535 Evaluate side-chains 97 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 58 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 106 optimal weight: 50.0000 chunk 125 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 175 optimal weight: 30.0000 chunk 130 optimal weight: 0.0060 chunk 23 optimal weight: 6.9990 overall best weight: 2.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN H 60 ASN 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 = 0.3675 r_free = 0.3675 target = 0.071726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035378 restraints weight = 133363.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.035695 restraints weight = 66590.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035777 restraints weight = 44294.193| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19616 Z= 0.167 Angle : 0.582 10.852 27840 Z= 0.334 Chirality : 0.038 0.167 3119 Planarity : 0.004 0.062 2501 Dihedral : 29.319 176.522 5115 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1530 helix: 1.71 (0.20), residues: 625 sheet: 0.89 (0.29), residues: 300 loop : 0.56 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.009 0.001 HIS K 178 PHE 0.010 0.001 PHE E 104 TYR 0.026 0.001 TYR H 80 ARG 0.005 0.000 ARG M 282 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1015) hydrogen bonds : angle 3.77177 ( 2529) covalent geometry : bond 0.00367 (19616) covalent geometry : angle 0.58225 (27840) ********************** 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 127 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9641 (mm-30) cc_final: 0.9428 (mm-30) REVERT: A 97 GLU cc_start: 0.9055 (pp20) cc_final: 0.8670 (pp20) REVERT: A 120 MET cc_start: 0.8827 (mmp) cc_final: 0.8292 (mmm) REVERT: B 74 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9251 (tm-30) REVERT: B 84 MET cc_start: 0.9183 (tpp) cc_final: 0.8967 (mmm) REVERT: C 90 ASP cc_start: 0.8698 (t0) cc_final: 0.8430 (t0) REVERT: D 65 ASP cc_start: 0.9386 (t0) cc_final: 0.9112 (t0) REVERT: D 97 LEU cc_start: 0.9642 (mt) cc_final: 0.9392 (mt) REVERT: E 90 MET cc_start: 0.9445 (mmm) cc_final: 0.9086 (mmp) REVERT: E 92 LEU cc_start: 0.9509 (tp) cc_final: 0.9225 (tt) REVERT: E 96 CYS cc_start: 0.9367 (m) cc_final: 0.8956 (m) REVERT: E 106 ASP cc_start: 0.9226 (m-30) cc_final: 0.8930 (m-30) REVERT: E 123 ASP cc_start: 0.8789 (m-30) cc_final: 0.8509 (m-30) REVERT: F 79 LYS cc_start: 0.9393 (mtmm) cc_final: 0.9068 (mtmm) REVERT: G 68 ASN cc_start: 0.9410 (m-40) cc_final: 0.9016 (m110) REVERT: G 90 ASP cc_start: 0.8308 (t70) cc_final: 0.8087 (t0) REVERT: K 193 HIS cc_start: 0.1371 (t-90) cc_final: 0.1062 (t-90) REVERT: K 236 TYR cc_start: 0.5148 (m-80) cc_final: 0.4864 (m-80) REVERT: K 246 MET cc_start: 0.0654 (mtt) cc_final: 0.0323 (mtm) REVERT: N 133 MET cc_start: 0.6730 (ppp) cc_final: 0.6413 (ppp) REVERT: N 160 MET cc_start: -0.1841 (tmm) cc_final: -0.2207 (tmm) REVERT: N 237 MET cc_start: 0.8021 (mmm) cc_final: 0.7819 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2975 time to fit residues: 59.0800 Evaluate side-chains 91 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** 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 = 0.3693 r_free = 0.3693 target = 0.072217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036501 restraints weight = 133271.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036167 restraints weight = 64809.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036205 restraints weight = 39281.146| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19616 Z= 0.160 Angle : 0.582 10.650 27840 Z= 0.333 Chirality : 0.038 0.163 3119 Planarity : 0.004 0.058 2501 Dihedral : 29.246 176.295 5115 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1530 helix: 1.77 (0.20), residues: 625 sheet: 0.91 (0.29), residues: 300 loop : 0.59 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.008 0.001 HIS K 178 PHE 0.012 0.001 PHE L 270 TYR 0.024 0.001 TYR H 80 ARG 0.014 0.000 ARG M 290 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1015) hydrogen bonds : angle 3.74118 ( 2529) covalent geometry : bond 0.00353 (19616) covalent geometry : angle 0.58168 (27840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8372.67 seconds wall clock time: 145 minutes 27.37 seconds (8727.37 seconds total)