Starting phenix.real_space_refine on Wed Sep 25 04:34:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/09_2024/6vsa_21373.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/09_2024/6vsa_21373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/09_2024/6vsa_21373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/09_2024/6vsa_21373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/09_2024/6vsa_21373.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/09_2024/6vsa_21373.cif" } resolution = 2.32 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= 0.020 sd= 0.129 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6230 2.51 5 N 1610 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9712 Number of models: 1 Model: "" Number of chains: 10 Chain: "V" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "W" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "X" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "Y" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "Z" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "V" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "W" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "X" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Z" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 6.43, per 1000 atoms: 0.66 Number of scatterers: 9712 At special positions: 0 Unit cell: (97.2, 99.36, 76.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1822 8.00 N 1610 7.00 C 6230 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: 3.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 46.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'V' and resid 21 through 28 Processing helix chain 'V' and resid 29 through 53 Processing helix chain 'V' and resid 78 through 91 Processing helix chain 'V' and resid 92 through 96 Processing helix chain 'V' and resid 124 through 132 Processing helix chain 'V' and resid 160 through 178 removed outlier: 3.534A pdb=" N ALA V 170 " --> pdb=" O GLU V 166 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR V 178 " --> pdb=" O THR V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 217 removed outlier: 3.804A pdb=" N LYS V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 225 Processing helix chain 'V' and resid 238 through 240 No H-bonds generated for 'chain 'V' and resid 238 through 240' Processing helix chain 'V' and resid 241 through 246 Processing helix chain 'W' and resid 21 through 28 Processing helix chain 'W' and resid 29 through 53 Processing helix chain 'W' and resid 78 through 91 Processing helix chain 'W' and resid 92 through 96 Processing helix chain 'W' and resid 124 through 132 Processing helix chain 'W' and resid 160 through 178 removed outlier: 3.537A pdb=" N ALA W 170 " --> pdb=" O GLU W 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR W 178 " --> pdb=" O THR W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 217 removed outlier: 3.806A pdb=" N LYS W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 225 Processing helix chain 'W' and resid 238 through 240 No H-bonds generated for 'chain 'W' and resid 238 through 240' Processing helix chain 'W' and resid 241 through 246 Processing helix chain 'X' and resid 21 through 28 Processing helix chain 'X' and resid 29 through 53 Processing helix chain 'X' and resid 78 through 91 Processing helix chain 'X' and resid 92 through 96 Processing helix chain 'X' and resid 124 through 132 Processing helix chain 'X' and resid 160 through 178 removed outlier: 3.537A pdb=" N ALA X 170 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR X 178 " --> pdb=" O THR X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 217 removed outlier: 3.808A pdb=" N LYS X 210 " --> pdb=" O ALA X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 225 Processing helix chain 'X' and resid 238 through 240 No H-bonds generated for 'chain 'X' and resid 238 through 240' Processing helix chain 'X' and resid 241 through 246 Processing helix chain 'Y' and resid 21 through 28 Processing helix chain 'Y' and resid 29 through 53 Processing helix chain 'Y' and resid 78 through 91 Processing helix chain 'Y' and resid 92 through 96 Processing helix chain 'Y' and resid 124 through 132 removed outlier: 5.975A pdb=" N ARG Y 130 " --> pdb=" O GLU Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 178 removed outlier: 3.533A pdb=" N ALA Y 170 " --> pdb=" O GLU Y 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR Y 178 " --> pdb=" O THR Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 217 removed outlier: 3.807A pdb=" N LYS Y 210 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 219 through 225 Processing helix chain 'Y' and resid 238 through 240 No H-bonds generated for 'chain 'Y' and resid 238 through 240' Processing helix chain 'Y' and resid 241 through 246 Processing helix chain 'Z' and resid 21 through 28 Processing helix chain 'Z' and resid 29 through 53 Processing helix chain 'Z' and resid 78 through 91 Processing helix chain 'Z' and resid 92 through 96 Processing helix chain 'Z' and resid 124 through 132 Processing helix chain 'Z' and resid 160 through 178 removed outlier: 3.537A pdb=" N ALA Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR Z 178 " --> pdb=" O THR Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 206 through 217 removed outlier: 3.804A pdb=" N LYS Z 210 " --> pdb=" O ALA Z 206 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 225 Processing helix chain 'Z' and resid 238 through 240 No H-bonds generated for 'chain 'Z' and resid 238 through 240' Processing helix chain 'Z' and resid 241 through 246 Processing sheet with id=AA1, first strand: chain 'V' and resid 226 through 228 removed outlier: 4.169A pdb=" N TRP V 11 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR V 19 " --> pdb=" O PRO V 100 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU V 109 " --> pdb=" O ILE V 186 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE V 186 " --> pdb=" O GLU V 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 150 through 151 Processing sheet with id=AA3, first strand: chain 'W' and resid 226 through 228 removed outlier: 5.929A pdb=" N ASP W 9 " --> pdb=" O LEU W 110 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU W 110 " --> pdb=" O ASP W 9 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP W 11 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR W 19 " --> pdb=" O PRO W 100 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU W 109 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE W 186 " --> pdb=" O GLU W 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'W' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'X' and resid 226 through 228 removed outlier: 5.945A pdb=" N ASP X 9 " --> pdb=" O LEU X 110 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU X 110 " --> pdb=" O ASP X 9 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP X 11 " --> pdb=" O VAL X 108 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR X 19 " --> pdb=" O PRO X 100 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU X 109 " --> pdb=" O ILE X 186 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE X 186 " --> pdb=" O GLU X 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 150 through 151 Processing sheet with id=AA7, first strand: chain 'Y' and resid 226 through 228 removed outlier: 5.950A pdb=" N ASP Y 9 " --> pdb=" O LEU Y 110 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU Y 110 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP Y 11 " --> pdb=" O VAL Y 108 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR Y 19 " --> pdb=" O PRO Y 100 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Y 109 " --> pdb=" O ILE Y 186 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE Y 186 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'Z' and resid 226 through 228 removed outlier: 5.947A pdb=" N ASP Z 9 " --> pdb=" O LEU Z 110 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU Z 110 " --> pdb=" O ASP Z 9 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP Z 11 " --> pdb=" O VAL Z 108 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR Z 19 " --> pdb=" O PRO Z 100 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Z 109 " --> pdb=" O ILE Z 186 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE Z 186 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 150 through 151 569 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 3.46 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: 2519 1.33 - 1.46: 3125 1.46 - 1.59: 4186 1.59 - 1.73: 0 1.73 - 1.86: 90 Bond restraints: 9920 Sorted by residual: bond pdb=" CA SER W 230 " pdb=" CB SER W 230 " ideal model delta sigma weight residual 1.529 1.435 0.094 1.58e-02 4.01e+03 3.57e+01 bond pdb=" CA SER X 230 " pdb=" CB SER X 230 " ideal model delta sigma weight residual 1.529 1.436 0.093 1.58e-02 4.01e+03 3.45e+01 bond pdb=" CA SER Z 230 " pdb=" CB SER Z 230 " ideal model delta sigma weight residual 1.529 1.436 0.093 1.58e-02 4.01e+03 3.44e+01 bond pdb=" CA SER Y 230 " pdb=" CB SER Y 230 " ideal model delta sigma weight residual 1.529 1.438 0.092 1.58e-02 4.01e+03 3.36e+01 bond pdb=" CA SER V 230 " pdb=" CB SER V 230 " ideal model delta sigma weight residual 1.529 1.439 0.090 1.58e-02 4.01e+03 3.25e+01 ... (remaining 9915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 12233 3.82 - 7.63: 1087 7.63 - 11.45: 95 11.45 - 15.27: 9 15.27 - 19.09: 1 Bond angle restraints: 13425 Sorted by residual: angle pdb=" CA PRO V 121 " pdb=" N PRO V 121 " pdb=" CD PRO V 121 " ideal model delta sigma weight residual 112.00 99.12 12.88 1.40e+00 5.10e-01 8.47e+01 angle pdb=" CB GLU W 31 " pdb=" CG GLU W 31 " pdb=" CD GLU W 31 " ideal model delta sigma weight residual 112.60 127.26 -14.66 1.70e+00 3.46e-01 7.43e+01 angle pdb=" CB ARG Z 169 " pdb=" CG ARG Z 169 " pdb=" CD ARG Z 169 " ideal model delta sigma weight residual 111.30 130.39 -19.09 2.30e+00 1.89e-01 6.89e+01 angle pdb=" CA THR Y 19 " pdb=" CB THR Y 19 " pdb=" OG1 THR Y 19 " ideal model delta sigma weight residual 109.60 98.34 11.26 1.50e+00 4.44e-01 5.63e+01 angle pdb=" CG ARG X 164 " pdb=" CD ARG X 164 " pdb=" NE ARG X 164 " ideal model delta sigma weight residual 112.00 97.79 14.21 2.20e+00 2.07e-01 4.17e+01 ... (remaining 13420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 5006 18.08 - 36.15: 617 36.15 - 54.23: 175 54.23 - 72.31: 33 72.31 - 90.38: 19 Dihedral angle restraints: 5850 sinusoidal: 2405 harmonic: 3445 Sorted by residual: dihedral pdb=" C MET Z 146 " pdb=" N MET Z 146 " pdb=" CA MET Z 146 " pdb=" CB MET Z 146 " ideal model delta harmonic sigma weight residual -122.60 -103.03 -19.57 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" N MET Z 146 " pdb=" C MET Z 146 " pdb=" CA MET Z 146 " pdb=" CB MET Z 146 " ideal model delta harmonic sigma weight residual 122.80 104.77 18.03 0 2.50e+00 1.60e-01 5.20e+01 dihedral pdb=" C CYS X 142 " pdb=" N CYS X 142 " pdb=" CA CYS X 142 " pdb=" CB CYS X 142 " ideal model delta harmonic sigma weight residual -122.60 -106.68 -15.92 0 2.50e+00 1.60e-01 4.05e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.555: 1428 0.555 - 1.111: 1 1.111 - 1.666: 0 1.666 - 2.221: 0 2.221 - 2.777: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CB VAL Y 127 " pdb=" CA VAL Y 127 " pdb=" CG1 VAL Y 127 " pdb=" CG2 VAL Y 127 " both_signs ideal model delta sigma weight residual False -2.63 0.15 -2.78 2.00e-01 2.50e+01 1.93e+02 chirality pdb=" CA GLU W 31 " pdb=" N GLU W 31 " pdb=" C GLU W 31 " pdb=" CB GLU W 31 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA MET Z 146 " pdb=" N MET Z 146 " pdb=" C MET Z 146 " pdb=" CB MET Z 146 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.51 2.00e-01 2.50e+01 6.63e+00 ... (remaining 1427 not shown) Planarity restraints: 1705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR Y 178 " -0.040 2.00e-02 2.50e+03 8.18e-02 6.70e+01 pdb=" C TYR Y 178 " 0.142 2.00e-02 2.50e+03 pdb=" O TYR Y 178 " -0.053 2.00e-02 2.50e+03 pdb=" N ALA Y 179 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 225 " 0.012 2.00e-02 2.50e+03 4.14e-02 3.00e+01 pdb=" CG PHE Z 225 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 225 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 225 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 225 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 225 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE Z 225 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 225 " 0.011 2.00e-02 2.50e+03 4.12e-02 2.96e+01 pdb=" CG PHE V 225 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE V 225 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE V 225 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE V 225 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE V 225 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE V 225 " 0.078 2.00e-02 2.50e+03 ... (remaining 1702 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 245 2.62 - 3.19: 8760 3.19 - 3.76: 17303 3.76 - 4.33: 25745 4.33 - 4.90: 39699 Nonbonded interactions: 91752 Sorted by model distance: nonbonded pdb=" NZ LYS W 67 " pdb=" OD1 ASP Y 194 " model vdw 2.048 3.120 nonbonded pdb=" NZ LYS X 67 " pdb=" OD1 ASP Z 194 " model vdw 2.054 3.120 nonbonded pdb=" OD1 ASP X 194 " pdb=" NZ LYS Y 67 " model vdw 2.066 3.120 nonbonded pdb=" OD1 ASP V 194 " pdb=" NZ LYS Z 67 " model vdw 2.073 3.120 nonbonded pdb=" O GLY Y 65 " pdb=" O HOH Y 301 " model vdw 2.073 3.040 ... (remaining 91747 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 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.090 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 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 : 0.013 0.115 9920 Z= 0.861 Angle : 2.263 19.087 13425 Z= 1.465 Chirality : 0.159 2.777 1430 Planarity : 0.012 0.082 1705 Dihedral : 18.035 90.385 3630 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.44 % Allowed : 13.04 % Favored : 82.51 % Cbeta Deviations : 6.76 % 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: -1.58 (0.22), residues: 1155 helix: -1.92 (0.19), residues: 505 sheet: 0.61 (0.28), residues: 315 loop : -0.88 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.014 TRP W 25 HIS 0.030 0.008 HIS W 15 PHE 0.079 0.014 PHE Z 225 TYR 0.049 0.011 TYR X 157 ARG 0.038 0.004 ARG Y 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 101 time to evaluate : 1.146 Fit side-chains REVERT: V 6 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6902 (tp40) REVERT: W 6 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7073 (tp40) REVERT: X 6 GLN cc_start: 0.7057 (mp-120) cc_final: 0.6486 (tp40) REVERT: Y 6 GLN cc_start: 0.6896 (mp10) cc_final: 0.6242 (tp40) REVERT: Y 161 MET cc_start: 0.8707 (tmt) cc_final: 0.8477 (tmt) REVERT: Z 6 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6996 (tp40) outliers start: 46 outliers final: 5 residues processed: 134 average time/residue: 1.4649 time to fit residues: 208.4486 Evaluate side-chains 80 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain W residue 6 GLN Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 7 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 6 GLN W 6 GLN W 83 HIS W 163 GLN ** W 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 HIS Z 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9920 Z= 0.204 Angle : 0.590 6.891 13425 Z= 0.318 Chirality : 0.042 0.315 1430 Planarity : 0.005 0.038 1705 Dihedral : 5.825 37.606 1317 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 2.42 % Allowed : 17.00 % Favored : 80.58 % 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: -0.39 (0.23), residues: 1155 helix: 0.06 (0.21), residues: 520 sheet: -0.36 (0.25), residues: 365 loop : -0.22 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 156 HIS 0.002 0.001 HIS V 83 PHE 0.017 0.002 PHE Y 225 TYR 0.019 0.002 TYR Z 157 ARG 0.007 0.001 ARG Y 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.114 Fit side-chains REVERT: V 6 GLN cc_start: 0.7398 (mp10) cc_final: 0.6716 (pp30) REVERT: W 6 GLN cc_start: 0.7462 (mp10) cc_final: 0.6836 (pp30) REVERT: X 6 GLN cc_start: 0.7463 (mp-120) cc_final: 0.6690 (tm-30) REVERT: X 161 MET cc_start: 0.8713 (tmm) cc_final: 0.8340 (tmt) REVERT: Y 6 GLN cc_start: 0.7030 (mp10) cc_final: 0.6303 (tm-30) REVERT: Z 6 GLN cc_start: 0.7336 (mp10) cc_final: 0.6548 (tm-30) REVERT: Z 161 MET cc_start: 0.8686 (tmm) cc_final: 0.8477 (tmt) outliers start: 25 outliers final: 11 residues processed: 123 average time/residue: 1.2843 time to fit residues: 168.9971 Evaluate side-chains 94 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 160 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 123 GLN X 123 GLN ** X 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 163 GLN Y 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9920 Z= 0.339 Angle : 0.556 6.263 13425 Z= 0.298 Chirality : 0.043 0.390 1430 Planarity : 0.004 0.035 1705 Dihedral : 4.767 19.845 1302 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 2.61 % Allowed : 17.29 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.24), residues: 1155 helix: 0.77 (0.22), residues: 520 sheet: -0.10 (0.27), residues: 345 loop : 0.38 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 156 HIS 0.003 0.001 HIS W 58 PHE 0.013 0.002 PHE Z 143 TYR 0.018 0.002 TYR Z 97 ARG 0.004 0.001 ARG Y 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.029 Fit side-chains REVERT: V 6 GLN cc_start: 0.7341 (mp10) cc_final: 0.6722 (pp30) REVERT: V 194 ASP cc_start: 0.9299 (m-30) cc_final: 0.9049 (m-30) REVERT: W 6 GLN cc_start: 0.7402 (mp10) cc_final: 0.6789 (pp30) REVERT: X 6 GLN cc_start: 0.7334 (mp-120) cc_final: 0.6662 (tp40) REVERT: X 161 MET cc_start: 0.8739 (tmm) cc_final: 0.8397 (tmt) REVERT: Y 6 GLN cc_start: 0.7005 (mp10) cc_final: 0.6316 (tp40) REVERT: Z 6 GLN cc_start: 0.7360 (mp10) cc_final: 0.6725 (pp30) REVERT: Z 161 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8517 (tmt) outliers start: 27 outliers final: 15 residues processed: 98 average time/residue: 1.3039 time to fit residues: 137.0518 Evaluate side-chains 93 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 230 SER Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 161 MET Chi-restraints excluded: chain Z residue 230 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 0.0170 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 123 GLN X 163 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9920 Z= 0.181 Angle : 0.480 7.228 13425 Z= 0.252 Chirality : 0.040 0.303 1430 Planarity : 0.004 0.034 1705 Dihedral : 4.421 18.337 1301 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 3.09 % Allowed : 16.52 % Favored : 80.39 % 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 (0.24), residues: 1155 helix: 0.95 (0.22), residues: 540 sheet: -0.12 (0.27), residues: 345 loop : 0.39 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 156 HIS 0.002 0.001 HIS Z 83 PHE 0.009 0.001 PHE Y 195 TYR 0.014 0.001 TYR Z 97 ARG 0.004 0.000 ARG V 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 85 time to evaluate : 1.183 Fit side-chains REVERT: V 6 GLN cc_start: 0.7321 (mp10) cc_final: 0.6720 (pp30) REVERT: W 6 GLN cc_start: 0.7431 (mp10) cc_final: 0.6824 (pp30) REVERT: X 6 GLN cc_start: 0.7374 (mp-120) cc_final: 0.6640 (tp40) REVERT: Y 6 GLN cc_start: 0.7132 (mp10) cc_final: 0.6508 (pp30) REVERT: Z 6 GLN cc_start: 0.7376 (mp10) cc_final: 0.6734 (pp30) REVERT: Z 161 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8348 (tmt) outliers start: 32 outliers final: 10 residues processed: 107 average time/residue: 1.2332 time to fit residues: 141.9894 Evaluate side-chains 89 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 161 MET Chi-restraints excluded: chain Z residue 230 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 171 HIS W 163 GLN W 241 ASN X 123 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9920 Z= 0.273 Angle : 0.508 7.541 13425 Z= 0.268 Chirality : 0.041 0.342 1430 Planarity : 0.004 0.036 1705 Dihedral : 4.411 18.536 1300 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % Rotamer: Outliers : 3.00 % Allowed : 16.52 % Favored : 80.48 % 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: 0.65 (0.24), residues: 1155 helix: 1.08 (0.22), residues: 540 sheet: -0.35 (0.27), residues: 345 loop : 0.60 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 156 HIS 0.002 0.001 HIS V 83 PHE 0.011 0.001 PHE Y 143 TYR 0.015 0.002 TYR Z 97 ARG 0.002 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 76 time to evaluate : 1.288 Fit side-chains REVERT: V 6 GLN cc_start: 0.7307 (mp10) cc_final: 0.6718 (pp30) REVERT: W 6 GLN cc_start: 0.7250 (mp10) cc_final: 0.6682 (pp30) REVERT: X 6 GLN cc_start: 0.7320 (mp-120) cc_final: 0.6639 (tp40) REVERT: X 161 MET cc_start: 0.8664 (tmm) cc_final: 0.8309 (tmt) REVERT: Y 6 GLN cc_start: 0.7108 (mp10) cc_final: 0.6427 (tp40) REVERT: Y 194 ASP cc_start: 0.9171 (m-30) cc_final: 0.8945 (m-30) REVERT: Z 6 GLN cc_start: 0.7369 (mp10) cc_final: 0.6811 (pp30) REVERT: Z 161 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8485 (tmt) outliers start: 31 outliers final: 14 residues processed: 98 average time/residue: 1.3230 time to fit residues: 138.8865 Evaluate side-chains 87 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 230 SER Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 161 MET Chi-restraints excluded: chain Z residue 230 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 163 GLN X 123 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9920 Z= 0.337 Angle : 0.537 8.064 13425 Z= 0.281 Chirality : 0.042 0.349 1430 Planarity : 0.004 0.034 1705 Dihedral : 4.487 18.623 1300 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 2.51 % Allowed : 17.58 % Favored : 79.90 % 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: 0.72 (0.24), residues: 1155 helix: 1.14 (0.22), residues: 535 sheet: -0.16 (0.27), residues: 310 loop : 0.32 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 156 HIS 0.003 0.001 HIS W 58 PHE 0.011 0.001 PHE V 143 TYR 0.015 0.002 TYR Z 97 ARG 0.002 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 1.189 Fit side-chains REVERT: V 6 GLN cc_start: 0.7203 (mp10) cc_final: 0.6606 (pp30) REVERT: W 6 GLN cc_start: 0.7233 (mp10) cc_final: 0.6732 (pp30) REVERT: X 6 GLN cc_start: 0.7300 (mp-120) cc_final: 0.6656 (tp40) REVERT: X 161 MET cc_start: 0.8691 (tmm) cc_final: 0.8340 (tmt) REVERT: Y 6 GLN cc_start: 0.7136 (mp10) cc_final: 0.6462 (tp40) REVERT: Z 6 GLN cc_start: 0.7262 (mp10) cc_final: 0.6791 (pp30) REVERT: Z 161 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8434 (tmt) outliers start: 26 outliers final: 16 residues processed: 93 average time/residue: 1.2728 time to fit residues: 127.5190 Evaluate side-chains 85 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 230 SER Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 161 MET Chi-restraints excluded: chain Z residue 230 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 163 GLN W 163 GLN X 123 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9920 Z= 0.228 Angle : 0.487 7.928 13425 Z= 0.255 Chirality : 0.041 0.314 1430 Planarity : 0.003 0.035 1705 Dihedral : 4.364 17.591 1300 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 2.80 % Allowed : 17.78 % Favored : 79.42 % 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 (0.24), residues: 1155 helix: 1.19 (0.22), residues: 540 sheet: -0.30 (0.27), residues: 310 loop : 0.27 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 156 HIS 0.002 0.001 HIS Z 83 PHE 0.010 0.001 PHE Z 143 TYR 0.014 0.001 TYR Z 97 ARG 0.002 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 1.072 Fit side-chains REVERT: V 6 GLN cc_start: 0.7215 (mp10) cc_final: 0.6614 (pp30) REVERT: W 6 GLN cc_start: 0.7242 (mp10) cc_final: 0.6730 (pp30) REVERT: W 71 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9202 (tp) REVERT: W 194 ASP cc_start: 0.9216 (m-30) cc_final: 0.9015 (m-30) REVERT: X 6 GLN cc_start: 0.7266 (mp-120) cc_final: 0.6650 (tp40) REVERT: X 161 MET cc_start: 0.8697 (tmm) cc_final: 0.8357 (tmt) REVERT: Y 6 GLN cc_start: 0.7133 (mp10) cc_final: 0.6452 (tp40) REVERT: Y 194 ASP cc_start: 0.9167 (m-30) cc_final: 0.8929 (m-30) REVERT: Z 6 GLN cc_start: 0.7293 (mp10) cc_final: 0.6844 (pp30) REVERT: Z 161 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8399 (tmt) REVERT: Z 239 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9045 (mmp) outliers start: 29 outliers final: 15 residues processed: 94 average time/residue: 1.1745 time to fit residues: 119.1397 Evaluate side-chains 89 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 230 SER Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ASP Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 161 MET Chi-restraints excluded: chain Z residue 230 SER Chi-restraints excluded: chain Z residue 239 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 163 GLN X 123 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9920 Z= 0.328 Angle : 0.531 8.815 13425 Z= 0.275 Chirality : 0.042 0.367 1430 Planarity : 0.004 0.035 1705 Dihedral : 4.424 18.072 1300 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 2.22 % Allowed : 18.36 % Favored : 79.42 % 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: 0.62 (0.24), residues: 1155 helix: 1.16 (0.22), residues: 540 sheet: -0.40 (0.27), residues: 310 loop : 0.27 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 156 HIS 0.003 0.001 HIS W 58 PHE 0.010 0.001 PHE Z 143 TYR 0.014 0.002 TYR W 97 ARG 0.002 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 1.174 Fit side-chains REVERT: V 6 GLN cc_start: 0.7184 (mp10) cc_final: 0.6560 (pp30) REVERT: W 6 GLN cc_start: 0.7254 (mp10) cc_final: 0.6779 (pp30) REVERT: W 71 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9206 (tp) REVERT: X 6 GLN cc_start: 0.7251 (mp-120) cc_final: 0.6643 (tp40) REVERT: X 161 MET cc_start: 0.8721 (tmm) cc_final: 0.8387 (tmt) REVERT: Y 6 GLN cc_start: 0.7121 (mp10) cc_final: 0.6468 (tp40) REVERT: Z 6 GLN cc_start: 0.7292 (mp10) cc_final: 0.6826 (pp30) REVERT: Z 161 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8413 (tmt) REVERT: Z 239 MET cc_start: 0.9316 (mmp) cc_final: 0.9043 (mmp) outliers start: 23 outliers final: 15 residues processed: 89 average time/residue: 1.2256 time to fit residues: 118.4798 Evaluate side-chains 85 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 161 MET Chi-restraints excluded: chain Z residue 230 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 163 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9920 Z= 0.335 Angle : 0.530 8.600 13425 Z= 0.276 Chirality : 0.042 0.346 1430 Planarity : 0.004 0.035 1705 Dihedral : 4.452 18.024 1300 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 2.13 % Allowed : 18.55 % Favored : 79.32 % 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: 0.53 (0.24), residues: 1155 helix: 1.12 (0.22), residues: 540 sheet: -0.47 (0.27), residues: 310 loop : 0.19 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 156 HIS 0.003 0.001 HIS W 58 PHE 0.010 0.001 PHE Z 143 TYR 0.015 0.002 TYR Z 97 ARG 0.002 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 1.094 Fit side-chains REVERT: V 6 GLN cc_start: 0.7182 (mp10) cc_final: 0.6581 (pp30) REVERT: V 194 ASP cc_start: 0.9280 (m-30) cc_final: 0.9007 (m-30) REVERT: W 6 GLN cc_start: 0.7207 (mp10) cc_final: 0.6763 (pp30) REVERT: W 71 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9225 (tp) REVERT: X 6 GLN cc_start: 0.7251 (mp-120) cc_final: 0.6712 (tp40) REVERT: Y 6 GLN cc_start: 0.7149 (mp10) cc_final: 0.6496 (tp40) REVERT: Z 6 GLN cc_start: 0.7234 (mp10) cc_final: 0.6757 (pp30) REVERT: Z 161 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8403 (tmt) REVERT: Z 239 MET cc_start: 0.9306 (mmp) cc_final: 0.9063 (mmp) outliers start: 22 outliers final: 15 residues processed: 89 average time/residue: 1.2395 time to fit residues: 118.9048 Evaluate side-chains 86 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 161 MET Chi-restraints excluded: chain Z residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 163 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9920 Z= 0.221 Angle : 0.502 9.388 13425 Z= 0.258 Chirality : 0.041 0.335 1430 Planarity : 0.003 0.035 1705 Dihedral : 4.324 17.580 1300 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 2.03 % Allowed : 18.65 % Favored : 79.32 % 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: 0.61 (0.24), residues: 1155 helix: 1.21 (0.22), residues: 540 sheet: -0.43 (0.27), residues: 310 loop : 0.19 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 156 HIS 0.002 0.001 HIS V 83 PHE 0.009 0.001 PHE Z 143 TYR 0.013 0.001 TYR Z 97 ARG 0.002 0.000 ARG X 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 1.129 Fit side-chains REVERT: V 6 GLN cc_start: 0.7182 (mp10) cc_final: 0.6587 (pp30) REVERT: W 6 GLN cc_start: 0.7218 (mp10) cc_final: 0.6755 (pp30) REVERT: W 71 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9206 (tp) REVERT: X 6 GLN cc_start: 0.7295 (mp-120) cc_final: 0.6738 (tp40) REVERT: X 161 MET cc_start: 0.8628 (tmm) cc_final: 0.8326 (tmt) REVERT: Y 6 GLN cc_start: 0.7214 (mp10) cc_final: 0.6555 (tp40) REVERT: Y 194 ASP cc_start: 0.9149 (m-30) cc_final: 0.8910 (m-30) REVERT: Z 6 GLN cc_start: 0.7333 (mp10) cc_final: 0.6845 (pp30) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 1.2637 time to fit residues: 125.6790 Evaluate side-chains 87 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 85 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 244 SER Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.061562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050642 restraints weight = 35380.153| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.74 r_work: 0.2957 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9920 Z= 0.255 Angle : 0.509 9.293 13425 Z= 0.262 Chirality : 0.041 0.332 1430 Planarity : 0.003 0.035 1705 Dihedral : 4.326 17.611 1300 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 1.74 % Allowed : 19.03 % Favored : 79.23 % 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: 0.59 (0.24), residues: 1155 helix: 1.19 (0.22), residues: 540 sheet: -0.49 (0.27), residues: 310 loop : 0.21 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 156 HIS 0.002 0.001 HIS Z 83 PHE 0.010 0.001 PHE Z 143 TYR 0.013 0.001 TYR Z 97 ARG 0.005 0.000 ARG Z 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3133.48 seconds wall clock time: 56 minutes 5.92 seconds (3365.92 seconds total)