Starting phenix.real_space_refine on Wed Feb 14 13:48:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8i_31802/02_2024/7v8i_31802_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8i_31802/02_2024/7v8i_31802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8i_31802/02_2024/7v8i_31802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8i_31802/02_2024/7v8i_31802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8i_31802/02_2024/7v8i_31802_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8i_31802/02_2024/7v8i_31802_neut_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.077 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5956 2.51 5 N 1651 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9388 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2841 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 374} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1751 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 2978 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 14, 'TRANS': 392} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 101 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.27, per 1000 atoms: 0.56 Number of scatterers: 9388 At special positions: 0 Unit cell: (95, 86, 159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1651 7.00 C 5956 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 - 3.50 Amino acid : False - 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: 3.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 11 sheets defined 42.6% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 23 through 58 removed outlier: 4.517A pdb=" N SER C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 255 through 292 removed outlier: 3.663A pdb=" N SER C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 307 through 334 Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 362 through 380 removed outlier: 4.521A pdb=" N THR C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 78 through 87 Processing helix chain 'D' and resid 104 through 114 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.744A pdb=" N SER D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 148 through 160 Processing helix chain 'D' and resid 178 through 194 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 27 through 59 removed outlier: 4.133A pdb=" N ILE E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 36 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE E 59 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 123 through 126 No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 129 through 132 No H-bonds generated for 'chain 'E' and resid 129 through 132' Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 152 through 158 removed outlier: 5.161A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 208 through 214 Processing helix chain 'E' and resid 234 through 244 removed outlier: 3.858A pdb=" N VAL E 244 " --> pdb=" O ASP E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 293 removed outlier: 5.181A pdb=" N TYR E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N MET E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 305 Processing helix chain 'E' and resid 314 through 343 Processing helix chain 'E' and resid 349 through 355 removed outlier: 5.888A pdb=" N LEU E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 404 Proline residue: E 398 - end of helix Processing helix chain 'E' and resid 407 through 409 No H-bonds generated for 'chain 'E' and resid 407 through 409' Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 78 through 87 Processing helix chain 'F' and resid 104 through 114 Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 119 through 133 Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 148 through 161 Processing helix chain 'F' and resid 178 through 194 Processing helix chain 'F' and resid 206 through 210 Processing sheet with id= A, first strand: chain 'C' and resid 245 through 248 Processing sheet with id= B, first strand: chain 'C' and resid 176 through 185 removed outlier: 6.662A pdb=" N ALA C 169 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ARG C 182 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 10.984A pdb=" N PHE C 184 " --> pdb=" O MET C 165 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N MET C 165 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA C 169 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 15.544A pdb=" N THR C 98 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 30 through 32 Processing sheet with id= D, first strand: chain 'D' and resid 214 through 217 Processing sheet with id= E, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.550A pdb=" N LEU D 11 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS D 13 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS D 26 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 98 through 106 Processing sheet with id= G, first strand: chain 'E' and resid 165 through 169 Processing sheet with id= H, first strand: chain 'E' and resid 91 through 97 removed outlier: 6.811A pdb=" N LYS E 227 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA E 94 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA E 225 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY E 223 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 30 through 32 Processing sheet with id= J, first strand: chain 'F' and resid 214 through 218 removed outlier: 6.194A pdb=" N PHE F 199 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE F 40 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL F 201 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N GLY F 42 " --> pdb=" O VAL F 201 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 13 through 15 removed outlier: 7.861A pdb=" N TYR F 15 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP F 23 " --> pdb=" O TYR F 15 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1176 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: 2.56 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1901 1.33 - 1.45: 2032 1.45 - 1.57: 5510 1.57 - 1.69: 9 1.69 - 1.82: 90 Bond restraints: 9542 Sorted by residual: bond pdb=" O3A ANP F 302 " pdb=" PB ANP F 302 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP D 302 " pdb=" PB ANP D 302 " ideal model delta sigma weight residual 1.700 1.585 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" N3B ANP F 302 " pdb=" PG ANP F 302 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C4 ANP D 302 " pdb=" C5 ANP D 302 " ideal model delta sigma weight residual 1.387 1.469 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O5' ANP F 302 " pdb=" PA ANP F 302 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 9537 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.54: 299 106.54 - 114.21: 5632 114.21 - 121.89: 5047 121.89 - 129.56: 1946 129.56 - 137.24: 58 Bond angle restraints: 12982 Sorted by residual: angle pdb=" N ARG E 306 " pdb=" CA ARG E 306 " pdb=" C ARG E 306 " ideal model delta sigma weight residual 110.41 119.15 -8.74 1.23e+00 6.61e-01 5.05e+01 angle pdb=" N GLY F 18 " pdb=" CA GLY F 18 " pdb=" C GLY F 18 " ideal model delta sigma weight residual 111.36 119.66 -8.30 1.17e+00 7.31e-01 5.03e+01 angle pdb=" N VAL C 349 " pdb=" CA VAL C 349 " pdb=" C VAL C 349 " ideal model delta sigma weight residual 113.10 106.98 6.12 9.70e-01 1.06e+00 3.98e+01 angle pdb=" PB ANP F 302 " pdb=" N3B ANP F 302 " pdb=" PG ANP F 302 " ideal model delta sigma weight residual 126.95 109.48 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" PB ANP D 302 " pdb=" N3B ANP D 302 " pdb=" PG ANP D 302 " ideal model delta sigma weight residual 126.95 110.77 16.18 3.00e+00 1.11e-01 2.91e+01 ... (remaining 12977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 5608 35.39 - 70.79: 144 70.79 - 106.18: 18 106.18 - 141.57: 0 141.57 - 176.96: 2 Dihedral angle restraints: 5772 sinusoidal: 2186 harmonic: 3586 Sorted by residual: dihedral pdb=" O1A ANP D 302 " pdb=" O3A ANP D 302 " pdb=" PA ANP D 302 " pdb=" PB ANP D 302 " ideal model delta sinusoidal sigma weight residual 83.11 -93.85 176.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP F 302 " pdb=" O3A ANP F 302 " pdb=" PA ANP F 302 " pdb=" PB ANP F 302 " ideal model delta sinusoidal sigma weight residual 83.11 -72.13 155.24 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CA MET D 37 " pdb=" C MET D 37 " pdb=" N MET D 38 " pdb=" CA MET D 38 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1306 0.065 - 0.131: 223 0.131 - 0.196: 9 0.196 - 0.262: 5 0.262 - 0.327: 4 Chirality restraints: 1547 Sorted by residual: chirality pdb=" CA PRO E 74 " pdb=" N PRO E 74 " pdb=" C PRO E 74 " pdb=" CB PRO E 74 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ARG E 306 " pdb=" N ARG E 306 " pdb=" C ARG E 306 " pdb=" CB ARG E 306 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE E 280 " pdb=" CA ILE E 280 " pdb=" CG1 ILE E 280 " pdb=" CG2 ILE E 280 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1544 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 73 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO E 74 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 95 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO E 96 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 391 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO C 392 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 392 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 392 " 0.028 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 76 2.59 - 3.16: 8009 3.16 - 3.74: 14466 3.74 - 4.32: 19112 4.32 - 4.90: 30988 Nonbonded interactions: 72651 Sorted by model distance: nonbonded pdb="MG MG F 301 " pdb=" O3G ANP F 302 " model vdw 2.007 2.170 nonbonded pdb="MG MG D 301 " pdb=" O3G ANP D 302 " model vdw 2.021 2.170 nonbonded pdb="MG MG D 301 " pdb=" O2B ANP D 302 " model vdw 2.059 2.170 nonbonded pdb="MG MG F 301 " pdb=" O2B ANP F 302 " model vdw 2.079 2.170 nonbonded pdb=" O1B ANP F 302 " pdb=" O3G ANP F 302 " model vdw 2.081 3.040 ... (remaining 72646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 2 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 230 or resid 301 through 302)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 4.060 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.020 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 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 : 0.005 0.146 9542 Z= 0.315 Angle : 0.869 17.473 12982 Z= 0.458 Chirality : 0.050 0.327 1547 Planarity : 0.005 0.111 1664 Dihedral : 15.814 176.965 3464 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.91 % Favored : 95.77 % Rotamer: Outliers : 1.36 % Allowed : 0.42 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1253 helix: 0.29 (0.22), residues: 589 sheet: -0.19 (0.42), residues: 160 loop : -1.51 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 246 HIS 0.002 0.001 HIS D 96 PHE 0.014 0.001 PHE E 13 TYR 0.009 0.001 TYR C 128 ARG 0.007 0.000 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 344 MET cc_start: 0.1542 (tpp) cc_final: 0.1117 (tpt) REVERT: E 68 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6435 (tp) REVERT: E 69 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6024 (mt-10) REVERT: E 72 ASP cc_start: 0.4498 (OUTLIER) cc_final: 0.4091 (m-30) REVERT: F 46 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7071 (t) REVERT: F 147 SER cc_start: 0.8906 (p) cc_final: 0.8039 (p) REVERT: F 182 ASP cc_start: 0.6877 (m-30) cc_final: 0.6601 (m-30) REVERT: F 210 LYS cc_start: 0.7896 (tttp) cc_final: 0.7601 (tppt) outliers start: 13 outliers final: 0 residues processed: 206 average time/residue: 0.2031 time to fit residues: 59.1684 Evaluate side-chains 159 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain F residue 46 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.0050 chunk 111 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN D 86 ASN D 180 ASN E 122 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 9542 Z= 0.188 Angle : 0.610 7.423 12982 Z= 0.301 Chirality : 0.044 0.242 1547 Planarity : 0.005 0.116 1664 Dihedral : 11.471 174.595 1408 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.81 % Rotamer: Outliers : 1.99 % Allowed : 10.77 % Favored : 87.24 % 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: -0.80 (0.24), residues: 1253 helix: 0.18 (0.22), residues: 588 sheet: -0.07 (0.42), residues: 163 loop : -1.49 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 246 HIS 0.002 0.000 HIS F 26 PHE 0.023 0.001 PHE C 51 TYR 0.008 0.001 TYR E 260 ARG 0.003 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: D 110 MET cc_start: 0.8012 (tpp) cc_final: 0.7450 (tpp) REVERT: E 68 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.5863 (tp) REVERT: E 69 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: F 182 ASP cc_start: 0.7007 (m-30) cc_final: 0.6529 (m-30) REVERT: F 210 LYS cc_start: 0.7865 (tttp) cc_final: 0.7577 (tppt) REVERT: F 212 MET cc_start: 0.6437 (ttm) cc_final: 0.6107 (ttm) outliers start: 19 outliers final: 11 residues processed: 174 average time/residue: 0.1990 time to fit residues: 48.8129 Evaluate side-chains 162 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.0030 chunk 92 optimal weight: 0.5980 chunk 76 optimal weight: 0.0170 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN C 181 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 9542 Z= 0.169 Angle : 0.566 7.035 12982 Z= 0.279 Chirality : 0.042 0.214 1547 Planarity : 0.005 0.107 1664 Dihedral : 10.727 173.902 1405 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.62 % Allowed : 12.66 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.24), residues: 1253 helix: 0.18 (0.22), residues: 597 sheet: 0.04 (0.41), residues: 163 loop : -1.38 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 75 HIS 0.002 0.000 HIS D 53 PHE 0.009 0.001 PHE F 185 TYR 0.014 0.001 TYR C 199 ARG 0.007 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.015 Fit side-chains REVERT: C 262 MET cc_start: 0.6136 (ptp) cc_final: 0.5833 (ptt) REVERT: E 68 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.5705 (tp) REVERT: E 305 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4739 (pt) REVERT: F 182 ASP cc_start: 0.6951 (m-30) cc_final: 0.6568 (m-30) REVERT: F 210 LYS cc_start: 0.7756 (tttp) cc_final: 0.7509 (tppt) outliers start: 25 outliers final: 15 residues processed: 178 average time/residue: 0.2132 time to fit residues: 52.3698 Evaluate side-chains 166 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN C 218 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN D 180 ASN E 122 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9542 Z= 0.193 Angle : 0.581 11.462 12982 Z= 0.283 Chirality : 0.043 0.211 1547 Planarity : 0.005 0.106 1664 Dihedral : 10.237 175.209 1402 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 2.93 % Allowed : 15.06 % Favored : 82.01 % 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: 1253 helix: 0.14 (0.22), residues: 595 sheet: 0.12 (0.41), residues: 163 loop : -1.37 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 246 HIS 0.002 0.001 HIS D 96 PHE 0.011 0.001 PHE E 319 TYR 0.013 0.001 TYR E 258 ARG 0.008 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: C 245 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7829 (pttm) REVERT: E 68 ILE cc_start: 0.5983 (OUTLIER) cc_final: 0.5513 (tp) REVERT: E 305 LEU cc_start: 0.5044 (OUTLIER) cc_final: 0.4831 (pt) REVERT: F 182 ASP cc_start: 0.6925 (m-30) cc_final: 0.6533 (m-30) REVERT: F 210 LYS cc_start: 0.7759 (tttp) cc_final: 0.7486 (tppt) REVERT: F 212 MET cc_start: 0.6212 (ttm) cc_final: 0.5967 (ttm) outliers start: 28 outliers final: 18 residues processed: 171 average time/residue: 0.2294 time to fit residues: 54.1005 Evaluate side-chains 165 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 0 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 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 181 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9542 Z= 0.179 Angle : 0.560 8.831 12982 Z= 0.275 Chirality : 0.042 0.194 1547 Planarity : 0.004 0.103 1664 Dihedral : 9.956 175.462 1402 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 16.95 % Favored : 79.71 % 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: -0.67 (0.24), residues: 1253 helix: 0.17 (0.22), residues: 596 sheet: 0.19 (0.42), residues: 163 loop : -1.34 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 75 HIS 0.002 0.000 HIS F 204 PHE 0.012 0.001 PHE E 319 TYR 0.016 0.001 TYR C 199 ARG 0.009 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: C 245 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7867 (pttm) REVERT: D 212 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6932 (mpt) REVERT: E 68 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5488 (tp) REVERT: E 305 LEU cc_start: 0.4995 (OUTLIER) cc_final: 0.4770 (pt) REVERT: F 182 ASP cc_start: 0.6866 (m-30) cc_final: 0.6492 (m-30) REVERT: F 212 MET cc_start: 0.6275 (ttm) cc_final: 0.6059 (ttm) outliers start: 32 outliers final: 17 residues processed: 171 average time/residue: 0.2386 time to fit residues: 55.5953 Evaluate side-chains 166 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 30.0000 chunk 39 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9542 Z= 0.178 Angle : 0.573 11.837 12982 Z= 0.276 Chirality : 0.042 0.202 1547 Planarity : 0.004 0.101 1664 Dihedral : 9.925 175.712 1402 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 3.03 % Allowed : 17.99 % Favored : 78.97 % 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: 1253 helix: 0.22 (0.22), residues: 589 sheet: 0.20 (0.41), residues: 161 loop : -1.30 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 246 HIS 0.002 0.000 HIS E 201 PHE 0.011 0.001 PHE E 319 TYR 0.014 0.001 TYR F 15 ARG 0.007 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: C 245 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7888 (pttm) REVERT: D 212 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6990 (mpt) REVERT: E 68 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5484 (tp) REVERT: F 182 ASP cc_start: 0.6839 (m-30) cc_final: 0.6477 (m-30) outliers start: 29 outliers final: 21 residues processed: 172 average time/residue: 0.2222 time to fit residues: 53.1667 Evaluate side-chains 167 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.0270 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 74 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN C 247 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9542 Z= 0.178 Angle : 0.585 11.399 12982 Z= 0.282 Chirality : 0.042 0.189 1547 Planarity : 0.004 0.098 1664 Dihedral : 9.910 175.740 1402 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.24 % Allowed : 17.99 % Favored : 78.77 % 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: 1253 helix: 0.28 (0.22), residues: 581 sheet: 0.27 (0.42), residues: 161 loop : -1.38 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 246 HIS 0.003 0.000 HIS E 201 PHE 0.010 0.001 PHE E 319 TYR 0.016 0.001 TYR C 199 ARG 0.005 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 245 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7834 (pttm) REVERT: D 212 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7057 (mpt) REVERT: F 182 ASP cc_start: 0.6810 (m-30) cc_final: 0.6404 (m-30) REVERT: F 210 LYS cc_start: 0.7727 (tttp) cc_final: 0.7470 (tppt) outliers start: 31 outliers final: 22 residues processed: 177 average time/residue: 0.2176 time to fit residues: 53.1425 Evaluate side-chains 172 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 0.0470 chunk 80 optimal weight: 0.0070 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 9542 Z= 0.165 Angle : 0.598 10.569 12982 Z= 0.286 Chirality : 0.042 0.208 1547 Planarity : 0.004 0.095 1664 Dihedral : 9.848 174.542 1402 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.59 % Favored : 96.33 % Rotamer: Outliers : 2.30 % Allowed : 19.46 % Favored : 78.24 % 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: -0.57 (0.24), residues: 1253 helix: 0.36 (0.22), residues: 586 sheet: 0.21 (0.43), residues: 156 loop : -1.39 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP C 246 HIS 0.003 0.000 HIS D 141 PHE 0.016 0.001 PHE C 51 TYR 0.012 0.001 TYR E 258 ARG 0.003 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 245 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7870 (pttm) REVERT: D 212 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7010 (mpt) REVERT: E 12 ARG cc_start: 0.4995 (ppt170) cc_final: 0.4063 (tmt170) REVERT: E 305 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4724 (pt) REVERT: F 182 ASP cc_start: 0.6643 (m-30) cc_final: 0.6310 (m-30) REVERT: F 210 LYS cc_start: 0.7582 (tttp) cc_final: 0.7352 (tppt) outliers start: 22 outliers final: 16 residues processed: 169 average time/residue: 0.2131 time to fit residues: 50.0527 Evaluate side-chains 164 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9542 Z= 0.223 Angle : 0.649 11.170 12982 Z= 0.311 Chirality : 0.043 0.211 1547 Planarity : 0.004 0.093 1664 Dihedral : 9.879 176.134 1402 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.62 % Allowed : 20.08 % Favored : 77.30 % 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: -0.63 (0.24), residues: 1253 helix: 0.30 (0.22), residues: 585 sheet: 0.18 (0.43), residues: 156 loop : -1.40 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 75 HIS 0.002 0.001 HIS D 96 PHE 0.012 0.001 PHE E 319 TYR 0.019 0.001 TYR C 199 ARG 0.004 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 245 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7828 (pttm) REVERT: D 212 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7099 (mpt) REVERT: F 182 ASP cc_start: 0.6670 (m-30) cc_final: 0.6325 (m-30) REVERT: F 210 LYS cc_start: 0.7662 (tttp) cc_final: 0.7423 (tppt) outliers start: 25 outliers final: 23 residues processed: 162 average time/residue: 0.2234 time to fit residues: 50.0219 Evaluate side-chains 169 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 LYS Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 20.0000 chunk 55 optimal weight: 0.0770 chunk 81 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9542 Z= 0.195 Angle : 0.634 9.400 12982 Z= 0.305 Chirality : 0.043 0.223 1547 Planarity : 0.004 0.090 1664 Dihedral : 9.851 174.286 1402 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.59 % Favored : 96.33 % Rotamer: Outliers : 2.41 % Allowed : 20.71 % Favored : 76.88 % 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: 1253 helix: 0.30 (0.22), residues: 585 sheet: 0.13 (0.43), residues: 156 loop : -1.42 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 75 HIS 0.011 0.001 HIS E 201 PHE 0.010 0.001 PHE C 51 TYR 0.011 0.001 TYR E 258 ARG 0.003 0.000 ARG C 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 245 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7845 (pttm) REVERT: D 212 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7138 (mpt) REVERT: F 182 ASP cc_start: 0.6741 (m-30) cc_final: 0.6372 (m-30) REVERT: F 210 LYS cc_start: 0.7569 (tttp) cc_final: 0.7349 (tppt) outliers start: 23 outliers final: 18 residues processed: 161 average time/residue: 0.2327 time to fit residues: 51.1652 Evaluate side-chains 166 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** 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 = 0.4498 r_free = 0.4498 target = 0.205379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162993 restraints weight = 13223.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160407 restraints weight = 10625.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.160654 restraints weight = 9751.931| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9542 Z= 0.225 Angle : 0.643 9.424 12982 Z= 0.309 Chirality : 0.043 0.229 1547 Planarity : 0.005 0.088 1664 Dihedral : 9.870 175.198 1402 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 2.30 % Allowed : 20.92 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1253 helix: 0.23 (0.22), residues: 586 sheet: 0.09 (0.42), residues: 156 loop : -1.45 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 75 HIS 0.003 0.001 HIS E 201 PHE 0.011 0.001 PHE E 319 TYR 0.017 0.001 TYR C 199 ARG 0.004 0.000 ARG F 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1974.28 seconds wall clock time: 36 minutes 38.75 seconds (2198.75 seconds total)