Starting phenix.real_space_refine on Thu Nov 14 21:38:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ima_60686/11_2024/9ima_60686.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ima_60686/11_2024/9ima_60686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ima_60686/11_2024/9ima_60686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ima_60686/11_2024/9ima_60686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ima_60686/11_2024/9ima_60686.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ima_60686/11_2024/9ima_60686.cif" } resolution = 2.65 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= 0.030 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 51 5.16 5 C 4933 2.51 5 N 1182 2.21 5 O 1306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7472 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1989 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 239} Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1989 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 239} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.79, per 1000 atoms: 0.77 Number of scatterers: 7472 At special positions: 0 Unit cell: (62.814, 104.139, 146.29, 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 51 16.00 O 1306 8.00 N 1182 7.00 C 4933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 972.6 milliseconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 49.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.824A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.741A pdb=" N GLN C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.752A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'B' and resid 25 through 49 removed outlier: 3.996A pdb=" N ARG B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 59 through 82 removed outlier: 3.673A pdb=" N GLY B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 117 removed outlier: 4.730A pdb=" N GLY B 97 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 153 removed outlier: 3.719A pdb=" N SER B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN B 140 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.541A pdb=" N MET B 161 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 191 removed outlier: 3.608A pdb=" N THR B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 226 removed outlier: 3.562A pdb=" N GLY B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 238 through 257 removed outlier: 3.508A pdb=" N TYR B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.625A pdb=" N ARG B 267 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.542A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 82 removed outlier: 4.224A pdb=" N PHE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 119 removed outlier: 4.159A pdb=" N VAL A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 162 through 173 Processing helix chain 'A' and resid 174 through 190 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 199 through 226 removed outlier: 3.661A pdb=" N GLY A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.656A pdb=" N TYR A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.835A pdb=" N THR C 33 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 57 " --> pdb=" O ASN C 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.139A pdb=" N TYR C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 125 through 129 removed outlier: 4.727A pdb=" N ALA C 142 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 189 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY C 144 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C 187 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 146 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER C 185 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS C 148 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C 183 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 125 through 129 removed outlier: 4.727A pdb=" N ALA C 142 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 189 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY C 144 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C 187 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 146 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER C 185 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS C 148 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C 183 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 182 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 157 through 159 removed outlier: 3.791A pdb=" N LYS C 214 " --> pdb=" O CYS C 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.638A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.995A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 118 removed outlier: 3.767A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 153 through 154 445 hydrogen bonds defined for protein. 1245 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: 2.34 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2184 1.34 - 1.46: 1473 1.46 - 1.58: 3941 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 7668 Sorted by residual: bond pdb=" CA LYS C 219 " pdb=" CB LYS C 219 " ideal model delta sigma weight residual 1.513 1.550 -0.037 2.59e-02 1.49e+03 1.99e+00 bond pdb=" CA ILE B 24 " pdb=" CB ILE B 24 " ideal model delta sigma weight residual 1.540 1.559 -0.019 1.36e-02 5.41e+03 1.94e+00 bond pdb=" CB GLU D 187 " pdb=" CG GLU D 187 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" CA ILE B 24 " pdb=" C ILE B 24 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.72e+00 bond pdb=" C ALA B 89 " pdb=" N PRO B 90 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.61e+00 ... (remaining 7663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 10225 1.87 - 3.75: 207 3.75 - 5.62: 36 5.62 - 7.50: 16 7.50 - 9.37: 4 Bond angle restraints: 10488 Sorted by residual: angle pdb=" C GLY B 23 " pdb=" N ILE B 24 " pdb=" CA ILE B 24 " ideal model delta sigma weight residual 121.97 129.66 -7.69 1.80e+00 3.09e-01 1.82e+01 angle pdb=" CA GLN D 199 " pdb=" CB GLN D 199 " pdb=" CG GLN D 199 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" C MET A 157 " pdb=" N PHE A 158 " pdb=" CA PHE A 158 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C VAL A 219 " pdb=" N TRP A 220 " pdb=" CA TRP A 220 " ideal model delta sigma weight residual 120.68 115.32 5.36 1.70e+00 3.46e-01 9.94e+00 angle pdb=" C ILE A 258 " pdb=" N VAL A 259 " pdb=" CA VAL A 259 " ideal model delta sigma weight residual 120.33 122.77 -2.44 8.00e-01 1.56e+00 9.33e+00 ... (remaining 10483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4425 17.90 - 35.79: 313 35.79 - 53.69: 42 53.69 - 71.59: 9 71.59 - 89.49: 7 Dihedral angle restraints: 4796 sinusoidal: 2074 harmonic: 2722 Sorted by residual: dihedral pdb=" CA ASN D 137 " pdb=" C ASN D 137 " pdb=" N ASN D 138 " pdb=" CA ASN D 138 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB GLU C 138 " pdb=" CG GLU C 138 " pdb=" CD GLU C 138 " pdb=" OE1 GLU C 138 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA PHE A 158 " pdb=" C PHE A 158 " pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta harmonic sigma weight residual 180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 791 0.035 - 0.070: 311 0.070 - 0.105: 114 0.105 - 0.139: 39 0.139 - 0.174: 3 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA LEU B 60 " pdb=" N LEU B 60 " pdb=" C LEU B 60 " pdb=" CB LEU B 60 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1255 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 194 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO B 195 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 162 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 163 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 199 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C GLN D 199 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN D 199 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 200 " -0.009 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1957 2.81 - 3.33: 6779 3.33 - 3.86: 12273 3.86 - 4.38: 14656 4.38 - 4.90: 25006 Nonbonded interactions: 60671 Sorted by model distance: nonbonded pdb=" O LEU B 84 " pdb=" OG1 THR B 88 " model vdw 2.292 3.040 nonbonded pdb=" O GLN D 124 " pdb=" OG SER D 127 " model vdw 2.302 3.040 nonbonded pdb=" O CYS A 136 " pdb=" OH TYR A 176 " model vdw 2.311 3.040 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.316 3.040 nonbonded pdb=" ND1 HIS A 202 " pdb=" OE2 GLU A 261 " model vdw 2.341 3.120 ... (remaining 60666 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 'B' } 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=1.00 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: 3.340 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.470 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.003 0.041 7668 Z= 0.188 Angle : 0.696 9.374 10488 Z= 0.361 Chirality : 0.044 0.174 1258 Planarity : 0.006 0.052 1251 Dihedral : 12.294 89.486 3023 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 0.12 (0.27), residues: 925 helix: 0.75 (0.24), residues: 419 sheet: 0.60 (0.36), residues: 209 loop : -1.17 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 220 HIS 0.003 0.001 HIS B 110 PHE 0.019 0.002 PHE B 124 TYR 0.013 0.001 TYR D 140 ARG 0.009 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8773 (mm110) cc_final: 0.8464 (mm110) REVERT: C 46 GLU cc_start: 0.8689 (tt0) cc_final: 0.8261 (tt0) REVERT: C 214 LYS cc_start: 0.7651 (tppt) cc_final: 0.6677 (tppt) REVERT: D 3 GLN cc_start: 0.8349 (mm110) cc_final: 0.8117 (mp10) REVERT: D 42 LYS cc_start: 0.8378 (mppt) cc_final: 0.8057 (mmtp) REVERT: D 45 LYS cc_start: 0.8421 (mttt) cc_final: 0.8177 (mtpm) REVERT: D 93 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7708 (mtp85) REVERT: D 126 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7029 (pttp) REVERT: D 150 VAL cc_start: 0.7531 (t) cc_final: 0.7241 (p) REVERT: B 113 ASN cc_start: 0.8272 (t0) cc_final: 0.8042 (t160) REVERT: B 198 ASN cc_start: 0.8168 (t0) cc_final: 0.7808 (p0) REVERT: B 232 GLN cc_start: 0.7670 (mt0) cc_final: 0.7099 (mp-120) REVERT: A 50 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7636 (mptp) REVERT: A 116 LYS cc_start: 0.7939 (tttp) cc_final: 0.7649 (tttm) REVERT: A 233 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7798 (mmt90) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 1.4092 time to fit residues: 198.2523 Evaluate side-chains 92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 230 GLN B 249 ASN A 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7668 Z= 0.310 Angle : 0.609 7.470 10488 Z= 0.309 Chirality : 0.044 0.152 1258 Planarity : 0.005 0.048 1251 Dihedral : 7.388 59.661 1387 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.95 % Allowed : 7.30 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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 (0.28), residues: 925 helix: 1.34 (0.25), residues: 423 sheet: 0.60 (0.36), residues: 222 loop : -0.94 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 237 HIS 0.005 0.001 HIS D 189 PHE 0.017 0.002 PHE D 209 TYR 0.012 0.002 TYR C 150 ARG 0.004 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.810 Fit side-chains REVERT: C 43 GLN cc_start: 0.8741 (mm110) cc_final: 0.8433 (mm110) REVERT: C 46 GLU cc_start: 0.8853 (tt0) cc_final: 0.8476 (tt0) REVERT: C 57 ASP cc_start: 0.8121 (t70) cc_final: 0.7837 (t0) REVERT: C 67 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.5645 (ptt90) REVERT: D 3 GLN cc_start: 0.8369 (mm110) cc_final: 0.8122 (mp-120) REVERT: D 45 LYS cc_start: 0.8549 (mttt) cc_final: 0.8276 (mtpm) REVERT: D 126 LYS cc_start: 0.7700 (mtmt) cc_final: 0.7057 (pttp) REVERT: D 179 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6888 (tp) REVERT: D 199 GLN cc_start: 0.7996 (pp30) cc_final: 0.7765 (pp30) REVERT: B 157 MET cc_start: 0.6954 (mtm) cc_final: 0.6689 (mtt) REVERT: B 198 ASN cc_start: 0.8275 (t0) cc_final: 0.7948 (p0) REVERT: B 232 GLN cc_start: 0.7538 (mt0) cc_final: 0.6970 (mp-120) REVERT: A 50 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7829 (mptp) outliers start: 16 outliers final: 6 residues processed: 105 average time/residue: 1.3571 time to fit residues: 150.0644 Evaluate side-chains 93 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN D 155 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7668 Z= 0.177 Angle : 0.521 8.295 10488 Z= 0.266 Chirality : 0.041 0.136 1258 Planarity : 0.004 0.040 1251 Dihedral : 7.019 58.327 1387 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.95 % Allowed : 9.61 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.02 (0.28), residues: 925 helix: 1.75 (0.25), residues: 421 sheet: 0.67 (0.36), residues: 222 loop : -0.92 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 220 HIS 0.004 0.001 HIS D 189 PHE 0.016 0.001 PHE D 209 TYR 0.008 0.001 TYR D 91 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.918 Fit side-chains REVERT: C 43 GLN cc_start: 0.8733 (mm110) cc_final: 0.8421 (mm110) REVERT: C 46 GLU cc_start: 0.8840 (tt0) cc_final: 0.8477 (tt0) REVERT: C 57 ASP cc_start: 0.8143 (t70) cc_final: 0.7853 (t0) REVERT: C 67 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.5473 (ptt90) REVERT: D 3 GLN cc_start: 0.8356 (mm110) cc_final: 0.8108 (mp-120) REVERT: D 45 LYS cc_start: 0.8515 (mttt) cc_final: 0.8242 (mtpm) REVERT: D 126 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7124 (pttp) REVERT: D 155 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: D 179 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7002 (tp) REVERT: B 157 MET cc_start: 0.6895 (mtm) cc_final: 0.6566 (mtt) REVERT: B 198 ASN cc_start: 0.8254 (t0) cc_final: 0.7934 (p0) REVERT: B 232 GLN cc_start: 0.7525 (mt0) cc_final: 0.6981 (mp-120) REVERT: B 263 CYS cc_start: 0.8507 (m) cc_final: 0.8220 (m) outliers start: 16 outliers final: 5 residues processed: 102 average time/residue: 1.4577 time to fit residues: 156.2941 Evaluate side-chains 88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 86 GLN B 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7668 Z= 0.268 Angle : 0.562 8.149 10488 Z= 0.285 Chirality : 0.043 0.143 1258 Planarity : 0.004 0.042 1251 Dihedral : 7.267 59.929 1387 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.31 % Allowed : 9.85 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 0.99 (0.28), residues: 925 helix: 1.74 (0.25), residues: 423 sheet: 0.66 (0.36), residues: 222 loop : -1.01 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 220 HIS 0.002 0.001 HIS A 202 PHE 0.020 0.002 PHE D 209 TYR 0.010 0.001 TYR D 91 ARG 0.005 0.000 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8730 (mm110) cc_final: 0.8426 (mm110) REVERT: C 46 GLU cc_start: 0.8839 (tt0) cc_final: 0.8467 (tt0) REVERT: C 57 ASP cc_start: 0.8154 (t70) cc_final: 0.7845 (t0) REVERT: C 67 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.5669 (ptt90) REVERT: D 45 LYS cc_start: 0.8534 (mttt) cc_final: 0.8254 (mtpm) REVERT: D 126 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7124 (pttp) REVERT: D 179 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6895 (tp) REVERT: B 157 MET cc_start: 0.7000 (mtm) cc_final: 0.6645 (mtt) REVERT: B 232 GLN cc_start: 0.7546 (mt0) cc_final: 0.6999 (mp-120) outliers start: 19 outliers final: 9 residues processed: 98 average time/residue: 1.4020 time to fit residues: 144.7289 Evaluate side-chains 91 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 86 GLN B 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 7668 Z= 0.490 Angle : 0.676 8.647 10488 Z= 0.341 Chirality : 0.048 0.159 1258 Planarity : 0.005 0.060 1251 Dihedral : 7.758 57.845 1387 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 2.80 % Allowed : 10.46 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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 (0.28), residues: 925 helix: 1.35 (0.25), residues: 423 sheet: 0.47 (0.36), residues: 224 loop : -1.27 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 220 HIS 0.002 0.001 HIS A 202 PHE 0.024 0.002 PHE D 209 TYR 0.013 0.002 TYR C 95 ARG 0.004 0.001 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8747 (mm110) cc_final: 0.8441 (mm110) REVERT: C 46 GLU cc_start: 0.8837 (tt0) cc_final: 0.8520 (tt0) REVERT: C 57 ASP cc_start: 0.8092 (t70) cc_final: 0.7745 (t0) REVERT: C 67 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.5603 (ptt90) REVERT: D 45 LYS cc_start: 0.8556 (mttt) cc_final: 0.8260 (mtpm) REVERT: D 179 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6813 (tp) REVERT: B 157 MET cc_start: 0.7149 (mtm) cc_final: 0.6793 (mtt) outliers start: 23 outliers final: 11 residues processed: 100 average time/residue: 1.3362 time to fit residues: 140.8352 Evaluate side-chains 91 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 86 GLN B 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7668 Z= 0.208 Angle : 0.539 8.063 10488 Z= 0.276 Chirality : 0.042 0.152 1258 Planarity : 0.004 0.040 1251 Dihedral : 7.246 59.916 1387 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.68 % Rotamer: Outliers : 1.82 % Allowed : 11.80 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 0.90 (0.28), residues: 925 helix: 1.74 (0.25), residues: 423 sheet: 0.56 (0.35), residues: 225 loop : -1.13 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 220 HIS 0.002 0.001 HIS D 189 PHE 0.017 0.001 PHE D 209 TYR 0.009 0.001 TYR D 91 ARG 0.006 0.000 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.701 Fit side-chains REVERT: C 43 GLN cc_start: 0.8713 (mm110) cc_final: 0.8415 (mm110) REVERT: C 46 GLU cc_start: 0.8820 (tt0) cc_final: 0.8451 (tt0) REVERT: C 57 ASP cc_start: 0.8164 (t70) cc_final: 0.7826 (t0) REVERT: C 67 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.5528 (ptt90) REVERT: D 45 LYS cc_start: 0.8487 (mttt) cc_final: 0.8211 (mtpm) REVERT: D 179 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6964 (tp) REVERT: B 157 MET cc_start: 0.6982 (mtm) cc_final: 0.6606 (mtt) outliers start: 15 outliers final: 6 residues processed: 93 average time/residue: 1.2795 time to fit residues: 125.7650 Evaluate side-chains 84 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 236 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7668 Z= 0.234 Angle : 0.548 7.873 10488 Z= 0.279 Chirality : 0.042 0.180 1258 Planarity : 0.004 0.042 1251 Dihedral : 7.245 59.719 1387 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.68 % Rotamer: Outliers : 2.19 % Allowed : 12.17 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.03 (0.28), residues: 925 helix: 1.85 (0.25), residues: 423 sheet: 0.59 (0.36), residues: 224 loop : -1.06 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 220 HIS 0.004 0.001 HIS D 189 PHE 0.025 0.001 PHE D 209 TYR 0.010 0.001 TYR D 91 ARG 0.007 0.000 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8774 (mm110) cc_final: 0.8480 (mm110) REVERT: C 46 GLU cc_start: 0.8849 (tt0) cc_final: 0.8478 (tt0) REVERT: C 57 ASP cc_start: 0.8132 (t70) cc_final: 0.7802 (t0) REVERT: C 67 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.5700 (ptt90) REVERT: D 45 LYS cc_start: 0.8521 (mttt) cc_final: 0.8236 (mtpm) REVERT: D 179 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6995 (tp) REVERT: B 157 MET cc_start: 0.7001 (mtm) cc_final: 0.6636 (mtt) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 1.3254 time to fit residues: 130.1227 Evaluate side-chains 88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 156 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 overall best weight: 0.7716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 236 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7668 Z= 0.187 Angle : 0.525 7.958 10488 Z= 0.268 Chirality : 0.041 0.173 1258 Planarity : 0.004 0.040 1251 Dihedral : 7.105 59.847 1387 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 2.19 % Allowed : 12.41 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.15 (0.28), residues: 925 helix: 1.97 (0.25), residues: 423 sheet: 0.61 (0.36), residues: 224 loop : -0.99 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 220 HIS 0.005 0.001 HIS D 189 PHE 0.020 0.001 PHE D 209 TYR 0.008 0.001 TYR D 91 ARG 0.007 0.000 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.838 Fit side-chains REVERT: C 43 GLN cc_start: 0.8790 (mm110) cc_final: 0.8506 (mm110) REVERT: C 46 GLU cc_start: 0.8819 (tt0) cc_final: 0.8438 (tt0) REVERT: C 57 ASP cc_start: 0.8176 (t70) cc_final: 0.7849 (t0) REVERT: C 67 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.5527 (ptt90) REVERT: D 45 LYS cc_start: 0.8499 (mttt) cc_final: 0.8220 (mtpm) REVERT: D 179 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6899 (tp) REVERT: B 154 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.6233 (mpp-170) REVERT: B 157 MET cc_start: 0.6929 (mtm) cc_final: 0.6594 (mtt) outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 1.3169 time to fit residues: 130.8453 Evaluate side-chains 88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 156 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN B 86 GLN B 236 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7668 Z= 0.275 Angle : 0.563 7.765 10488 Z= 0.287 Chirality : 0.042 0.142 1258 Planarity : 0.004 0.042 1251 Dihedral : 7.263 58.843 1387 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 2.07 % Allowed : 12.90 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.06 (0.28), residues: 925 helix: 1.86 (0.25), residues: 423 sheet: 0.66 (0.36), residues: 222 loop : -1.05 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 220 HIS 0.004 0.001 HIS D 189 PHE 0.029 0.002 PHE D 209 TYR 0.010 0.002 TYR D 91 ARG 0.007 0.000 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8793 (mm110) cc_final: 0.8503 (mm110) REVERT: C 46 GLU cc_start: 0.8862 (tt0) cc_final: 0.8493 (tt0) REVERT: C 57 ASP cc_start: 0.8131 (t70) cc_final: 0.7798 (t0) REVERT: C 67 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.5681 (ptt90) REVERT: D 45 LYS cc_start: 0.8523 (mttt) cc_final: 0.8238 (mtpm) REVERT: D 145 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7819 (tmtt) REVERT: D 179 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6937 (tp) REVERT: B 157 MET cc_start: 0.7038 (mtm) cc_final: 0.6688 (mtt) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 1.3384 time to fit residues: 132.7794 Evaluate side-chains 90 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 236 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7668 Z= 0.287 Angle : 0.574 7.765 10488 Z= 0.291 Chirality : 0.043 0.141 1258 Planarity : 0.004 0.041 1251 Dihedral : 7.273 58.569 1387 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 1.82 % Allowed : 13.14 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.02 (0.28), residues: 925 helix: 1.84 (0.25), residues: 423 sheet: 0.61 (0.35), residues: 222 loop : -1.07 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 220 HIS 0.004 0.001 HIS D 189 PHE 0.032 0.002 PHE D 209 TYR 0.010 0.002 TYR D 91 ARG 0.008 0.000 ARG D 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8791 (mm110) cc_final: 0.8498 (mm110) REVERT: C 46 GLU cc_start: 0.8863 (tt0) cc_final: 0.8494 (tt0) REVERT: C 57 ASP cc_start: 0.8131 (t70) cc_final: 0.7792 (t0) REVERT: C 67 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.5680 (ptt90) REVERT: D 45 LYS cc_start: 0.8527 (mttt) cc_final: 0.8242 (mtpm) REVERT: D 145 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7759 (tttt) REVERT: D 179 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6937 (tp) REVERT: B 157 MET cc_start: 0.7049 (mtm) cc_final: 0.6695 (mtt) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 1.3972 time to fit residues: 132.5437 Evaluate side-chains 88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 236 GLN B 249 ASN A 86 GLN A 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.083591 restraints weight = 8895.650| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.98 r_work: 0.2811 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7668 Z= 0.208 Angle : 0.537 7.907 10488 Z= 0.273 Chirality : 0.041 0.139 1258 Planarity : 0.004 0.041 1251 Dihedral : 7.105 59.163 1387 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 1.95 % Allowed : 13.14 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.16 (0.28), residues: 925 helix: 1.99 (0.25), residues: 423 sheet: 0.61 (0.35), residues: 224 loop : -1.01 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 220 HIS 0.002 0.001 HIS D 189 PHE 0.027 0.001 PHE D 209 TYR 0.009 0.001 TYR D 91 ARG 0.008 0.000 ARG D 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.86 seconds wall clock time: 55 minutes 53.78 seconds (3353.78 seconds total)