Starting phenix.real_space_refine on Tue Feb 13 15:18:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/02_2024/7xbw_33107_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/02_2024/7xbw_33107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/02_2024/7xbw_33107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/02_2024/7xbw_33107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/02_2024/7xbw_33107_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/02_2024/7xbw_33107_updated.pdb" } resolution = 2.8 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= 0.005 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 42 5.16 5 C 4316 2.51 5 N 1087 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6663 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1657 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2394 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 323} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 352 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2260 Unusual residues: {'CLR': 3} Classifications: {'peptide': 288, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 278, None: 3} Not linked: pdbres="LYS R 310 " pdbres="CLR R 401 " Not linked: pdbres="CLR R 401 " pdbres="CLR R 402 " Not linked: pdbres="CLR R 402 " pdbres="CLR R 403 " Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 4.15, per 1000 atoms: 0.62 Number of scatterers: 6663 At special positions: 0 Unit cell: (107.635, 111.815, 73.15, 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 42 16.00 O 1218 8.00 N 1087 7.00 C 4316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 175 " distance=2.03 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 41.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 280 removed outlier: 4.063A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 310 removed outlier: 3.693A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 349 Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 30 through 35 removed outlier: 3.601A pdb=" N ASN D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 24 removed outlier: 3.686A pdb=" N GLU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'R' and resid 31 through 57 Processing helix chain 'R' and resid 65 through 91 Proline residue: R 85 - end of helix Processing helix chain 'R' and resid 99 through 131 Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 146 through 164 Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 181 through 185 removed outlier: 3.838A pdb=" N GLU R 185 " --> pdb=" O GLU R 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 181 through 185' Processing helix chain 'R' and resid 187 through 200 Processing helix chain 'R' and resid 202 through 221 Processing helix chain 'R' and resid 228 through 258 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 266 through 288 removed outlier: 4.531A pdb=" N LEU R 271 " --> pdb=" O ARG R 268 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG R 272 " --> pdb=" O LYS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 296 Processing helix chain 'R' and resid 298 through 309 Processing sheet with id= A, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.760A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 58 through 63 removed outlier: 6.916A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP D 63 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU D 69 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 103 through 105 removed outlier: 5.735A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 146 through 150 removed outlier: 6.763A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.973A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 201 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 203 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.563A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 296 through 298 Processing sheet with id= H, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.871A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 921 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: 1.74 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2115 1.34 - 1.46: 1643 1.46 - 1.58: 2993 1.58 - 1.70: 4 1.70 - 1.81: 55 Bond restraints: 6810 Sorted by residual: bond pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.464 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.463 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sigma weight residual 1.413 1.298 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C3 CLR R 401 " pdb=" O1 CLR R 401 " ideal model delta sigma weight residual 1.413 1.299 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 6805 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.89: 140 106.89 - 113.66: 3863 113.66 - 120.43: 2528 120.43 - 127.20: 2716 127.20 - 133.98: 65 Bond angle restraints: 9312 Sorted by residual: angle pdb=" CA PRO E 60 " pdb=" N PRO E 60 " pdb=" CD PRO E 60 " ideal model delta sigma weight residual 112.00 106.71 5.29 1.40e+00 5.10e-01 1.43e+01 angle pdb=" C TYR R 259 " pdb=" N ASP R 260 " pdb=" CA ASP R 260 " ideal model delta sigma weight residual 122.08 125.76 -3.68 1.47e+00 4.63e-01 6.27e+00 angle pdb=" CA LEU R 84 " pdb=" CB LEU R 84 " pdb=" CG LEU R 84 " ideal model delta sigma weight residual 116.30 124.93 -8.63 3.50e+00 8.16e-02 6.08e+00 angle pdb=" C PRO E 60 " pdb=" CA PRO E 60 " pdb=" CB PRO E 60 " ideal model delta sigma weight residual 110.00 112.72 -2.72 1.12e+00 7.97e-01 5.92e+00 angle pdb=" C PRO C 282 " pdb=" N LEU C 283 " pdb=" CA LEU C 283 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.81e+00 ... (remaining 9307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 3718 14.96 - 29.91: 286 29.91 - 44.87: 82 44.87 - 59.82: 8 59.82 - 74.78: 4 Dihedral angle restraints: 4098 sinusoidal: 1515 harmonic: 2583 Sorted by residual: dihedral pdb=" CA ASP D 170 " pdb=" CB ASP D 170 " pdb=" CG ASP D 170 " pdb=" OD1 ASP D 170 " ideal model delta sinusoidal sigma weight residual -30.00 -81.40 51.40 1 2.00e+01 2.50e-03 9.03e+00 dihedral pdb=" CA CYS R 102 " pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 175 " ideal model delta sinusoidal sigma weight residual 79.00 129.88 -50.88 1 2.00e+01 2.50e-03 8.86e+00 dihedral pdb=" CB ARG D 150 " pdb=" CG ARG D 150 " pdb=" CD ARG D 150 " pdb=" NE ARG D 150 " ideal model delta sinusoidal sigma weight residual 60.00 106.56 -46.56 3 1.50e+01 4.44e-03 8.35e+00 ... (remaining 4095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 858 0.043 - 0.087: 202 0.087 - 0.130: 59 0.130 - 0.173: 5 0.173 - 0.217: 3 Chirality restraints: 1127 Sorted by residual: chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1124 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 38 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO D 39 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 59 " 0.039 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO E 60 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 84 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO R 85 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 85 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 85 " 0.022 5.00e-02 4.00e+02 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1391 2.78 - 3.31: 6646 3.31 - 3.84: 11519 3.84 - 4.37: 13295 4.37 - 4.90: 23055 Nonbonded interactions: 55906 Sorted by model distance: nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR R 179 " pdb=" NH1 ARG R 191 " model vdw 2.258 2.520 nonbonded pdb=" OG1 THR D 86 " pdb=" OD1 ASN D 88 " model vdw 2.276 2.440 nonbonded pdb=" OD2 ASP C 200 " pdb=" OG1 THR C 202 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR D 145 " pdb=" OD2 ASP D 186 " model vdw 2.288 2.440 ... (remaining 55901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.850 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: 4.030 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 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 0.133 6810 Z= 0.310 Angle : 0.542 8.631 9312 Z= 0.271 Chirality : 0.042 0.217 1127 Planarity : 0.004 0.081 1155 Dihedral : 11.689 74.778 2419 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.30), residues: 874 helix: 2.46 (0.27), residues: 382 sheet: 0.54 (0.41), residues: 178 loop : -0.64 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 82 HIS 0.004 0.001 HIS R 285 PHE 0.020 0.001 PHE R 110 TYR 0.019 0.001 TYR R 90 ARG 0.004 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.692 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.0148 time to fit residues: 126.8396 Evaluate side-chains 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6810 Z= 0.342 Angle : 0.604 9.514 9312 Z= 0.314 Chirality : 0.043 0.161 1127 Planarity : 0.004 0.062 1155 Dihedral : 4.752 50.412 1125 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.87 % Allowed : 13.77 % Favored : 83.36 % 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: 0.90 (0.28), residues: 874 helix: 1.72 (0.26), residues: 386 sheet: 0.24 (0.38), residues: 188 loop : -0.59 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 82 HIS 0.006 0.002 HIS C 188 PHE 0.024 0.002 PHE R 110 TYR 0.015 0.002 TYR D 59 ARG 0.002 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.659 Fit side-chains REVERT: D 237 ASN cc_start: 0.7657 (t0) cc_final: 0.7410 (t0) REVERT: R 191 ARG cc_start: 0.6169 (ttt180) cc_final: 0.5922 (ttp80) outliers start: 19 outliers final: 5 residues processed: 124 average time/residue: 0.8515 time to fit residues: 112.9026 Evaluate side-chains 106 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain R residue 116 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6810 Z= 0.207 Angle : 0.522 11.110 9312 Z= 0.267 Chirality : 0.040 0.155 1127 Planarity : 0.004 0.055 1155 Dihedral : 4.560 52.062 1125 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.57 % Allowed : 18.00 % Favored : 79.43 % 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: 0.84 (0.29), residues: 874 helix: 1.74 (0.26), residues: 387 sheet: 0.20 (0.39), residues: 179 loop : -0.70 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 82 HIS 0.004 0.001 HIS C 188 PHE 0.024 0.002 PHE R 165 TYR 0.019 0.001 TYR R 90 ARG 0.007 0.001 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.863 Fit side-chains REVERT: C 9 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6834 (OUTLIER) REVERT: C 276 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6657 (pm20) REVERT: D 196 THR cc_start: 0.6993 (m) cc_final: 0.6761 (p) REVERT: D 237 ASN cc_start: 0.7500 (t0) cc_final: 0.7262 (t0) REVERT: D 263 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8307 (m) REVERT: D 270 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7995 (pp) REVERT: R 288 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7071 (pt) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 0.8722 time to fit residues: 105.8634 Evaluate side-chains 102 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6810 Z= 0.244 Angle : 0.545 9.913 9312 Z= 0.277 Chirality : 0.040 0.150 1127 Planarity : 0.004 0.050 1155 Dihedral : 4.613 55.597 1125 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.48 % Allowed : 20.27 % Favored : 76.25 % 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: 0.75 (0.28), residues: 874 helix: 1.72 (0.26), residues: 382 sheet: 0.11 (0.39), residues: 170 loop : -0.75 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 99 HIS 0.004 0.001 HIS R 285 PHE 0.024 0.002 PHE R 165 TYR 0.020 0.001 TYR R 90 ARG 0.006 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.764 Fit side-chains REVERT: C 198 MET cc_start: 0.7626 (mpp) cc_final: 0.7259 (mpp) REVERT: C 276 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6584 (pm20) REVERT: D 237 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7359 (t0) REVERT: R 192 ASN cc_start: 0.7266 (m-40) cc_final: 0.6911 (t0) outliers start: 23 outliers final: 12 residues processed: 123 average time/residue: 0.8589 time to fit residues: 113.3743 Evaluate side-chains 110 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 HIS ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6810 Z= 0.283 Angle : 0.578 11.642 9312 Z= 0.296 Chirality : 0.041 0.147 1127 Planarity : 0.004 0.048 1155 Dihedral : 4.705 49.073 1125 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.69 % Allowed : 21.18 % Favored : 74.13 % 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: 0.56 (0.28), residues: 874 helix: 1.54 (0.26), residues: 386 sheet: -0.03 (0.38), residues: 169 loop : -0.81 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 99 HIS 0.004 0.001 HIS R 285 PHE 0.021 0.002 PHE C 196 TYR 0.019 0.002 TYR R 90 ARG 0.005 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.731 Fit side-chains REVERT: C 276 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: D 237 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7443 (t0) REVERT: D 270 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8137 (pp) REVERT: R 284 SER cc_start: 0.7668 (t) cc_final: 0.7425 (m) outliers start: 31 outliers final: 14 residues processed: 120 average time/residue: 0.8262 time to fit residues: 106.6148 Evaluate side-chains 111 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6810 Z= 0.179 Angle : 0.528 11.115 9312 Z= 0.271 Chirality : 0.039 0.151 1127 Planarity : 0.003 0.046 1155 Dihedral : 4.487 50.383 1125 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.03 % Allowed : 23.15 % Favored : 73.83 % 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: 0.66 (0.29), residues: 874 helix: 1.69 (0.27), residues: 386 sheet: -0.09 (0.38), residues: 175 loop : -0.78 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 82 HIS 0.003 0.001 HIS D 183 PHE 0.027 0.001 PHE R 165 TYR 0.020 0.001 TYR R 90 ARG 0.008 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.761 Fit side-chains REVERT: C 276 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: D 46 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6727 (mmm-85) REVERT: D 237 ASN cc_start: 0.7572 (t0) cc_final: 0.7312 (t0) REVERT: D 263 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8335 (m) REVERT: D 270 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8085 (pp) REVERT: R 165 PHE cc_start: 0.7445 (p90) cc_final: 0.7235 (p90) outliers start: 20 outliers final: 12 residues processed: 116 average time/residue: 0.8333 time to fit residues: 103.9727 Evaluate side-chains 110 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6810 Z= 0.210 Angle : 0.542 10.096 9312 Z= 0.280 Chirality : 0.040 0.149 1127 Planarity : 0.004 0.045 1155 Dihedral : 4.515 52.749 1125 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.63 % Allowed : 23.30 % Favored : 73.07 % 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 (0.28), residues: 874 helix: 1.69 (0.26), residues: 386 sheet: -0.08 (0.38), residues: 170 loop : -0.81 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.003 0.001 HIS R 285 PHE 0.024 0.002 PHE R 165 TYR 0.023 0.001 TYR R 90 ARG 0.008 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.777 Fit side-chains REVERT: C 276 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: D 46 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6771 (mmm-85) REVERT: D 237 ASN cc_start: 0.7644 (t0) cc_final: 0.7372 (t0) REVERT: D 263 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8347 (m) REVERT: D 270 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8182 (pp) outliers start: 24 outliers final: 13 residues processed: 106 average time/residue: 0.8571 time to fit residues: 97.7249 Evaluate side-chains 108 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 73 optimal weight: 0.0670 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN R 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6810 Z= 0.193 Angle : 0.530 9.913 9312 Z= 0.273 Chirality : 0.039 0.149 1127 Planarity : 0.004 0.044 1155 Dihedral : 4.504 56.873 1125 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.93 % Allowed : 23.15 % Favored : 72.92 % 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 (0.28), residues: 874 helix: 1.81 (0.26), residues: 382 sheet: -0.21 (0.38), residues: 175 loop : -0.73 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 99 HIS 0.003 0.001 HIS D 183 PHE 0.014 0.001 PHE C 196 TYR 0.012 0.001 TYR R 90 ARG 0.010 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.758 Fit side-chains REVERT: C 276 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6460 (pm20) REVERT: D 46 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6741 (mmm-85) REVERT: D 237 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7358 (t0) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.7942 time to fit residues: 101.0201 Evaluate side-chains 112 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 136 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 50 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.0070 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6810 Z= 0.149 Angle : 0.518 12.336 9312 Z= 0.264 Chirality : 0.039 0.152 1127 Planarity : 0.004 0.046 1155 Dihedral : 4.376 59.592 1125 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.18 % Allowed : 24.21 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 874 helix: 1.84 (0.27), residues: 385 sheet: -0.05 (0.38), residues: 173 loop : -0.76 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 82 HIS 0.002 0.001 HIS D 183 PHE 0.019 0.001 PHE R 165 TYR 0.022 0.001 TYR R 90 ARG 0.010 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.684 Fit side-chains REVERT: C 32 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7399 (ttm-80) REVERT: C 276 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: D 46 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6719 (mmm-85) REVERT: D 52 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.7723 (mtt90) REVERT: D 237 ASN cc_start: 0.7518 (t0) cc_final: 0.7268 (t0) REVERT: D 263 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8322 (m) REVERT: D 269 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6401 (pp) REVERT: R 103 LYS cc_start: 0.7300 (ttmm) cc_final: 0.6966 (mmtm) REVERT: R 165 PHE cc_start: 0.7256 (p90) cc_final: 0.7039 (p90) REVERT: R 247 TYR cc_start: 0.7860 (t80) cc_final: 0.7654 (t80) outliers start: 21 outliers final: 11 residues processed: 115 average time/residue: 0.8757 time to fit residues: 107.6971 Evaluate side-chains 108 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 116 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6810 Z= 0.266 Angle : 0.592 12.669 9312 Z= 0.303 Chirality : 0.041 0.220 1127 Planarity : 0.004 0.044 1155 Dihedral : 4.725 57.373 1125 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.18 % Allowed : 24.05 % Favored : 72.77 % 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: 0.62 (0.28), residues: 874 helix: 1.60 (0.26), residues: 388 sheet: 0.00 (0.38), residues: 176 loop : -0.81 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 258 HIS 0.003 0.001 HIS D 311 PHE 0.026 0.002 PHE R 165 TYR 0.012 0.001 TYR R 90 ARG 0.009 0.001 ARG C 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.846 Fit side-chains REVERT: C 276 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6492 (pm20) REVERT: D 237 ASN cc_start: 0.7785 (t0) cc_final: 0.7485 (t0) REVERT: D 269 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6380 (pp) REVERT: R 165 PHE cc_start: 0.7515 (p90) cc_final: 0.7291 (p90) outliers start: 21 outliers final: 14 residues processed: 106 average time/residue: 0.8880 time to fit residues: 100.9431 Evaluate side-chains 106 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN ** R 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133309 restraints weight = 6969.029| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.93 r_work: 0.3374 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6810 Z= 0.230 Angle : 0.580 12.322 9312 Z= 0.297 Chirality : 0.041 0.185 1127 Planarity : 0.004 0.046 1155 Dihedral : 4.696 54.537 1125 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.33 % Allowed : 23.90 % Favored : 72.77 % 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: 0.58 (0.28), residues: 874 helix: 1.63 (0.26), residues: 381 sheet: 0.05 (0.39), residues: 168 loop : -0.90 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.003 0.001 HIS R 285 PHE 0.026 0.002 PHE R 165 TYR 0.025 0.001 TYR R 90 ARG 0.011 0.001 ARG C 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.16 seconds wall clock time: 53 minutes 14.83 seconds (3194.83 seconds total)