Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:21:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/04_2023/7xbw_33107_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/04_2023/7xbw_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_33107/04_2023/7xbw_33107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/04_2023/7xbw_33107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/04_2023/7xbw_33107_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbw_33107/04_2023/7xbw_33107_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.11, 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: 2.97 Conformation dependent library (CDL) restraints added in 1.2 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: 0.62 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: 3.00 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: 3569 14.96 - 29.91: 277 29.91 - 44.87: 72 44.87 - 59.82: 8 59.82 - 74.78: 4 Dihedral angle restraints: 3930 sinusoidal: 1347 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 3927 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: 0.940 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: 0.000 Extract box with map and model: 4.240 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.030 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.590 ------------------------------------------------------------------------------- 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 : 11.707 74.778 2251 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 % 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 *********************** 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 : 0.767 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.1248 time to fit residues: 140.5290 Evaluate side-chains 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0575 ------------------------------------------------------------------------------- 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: 0.7276 moved from start: 0.2700 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= 0.334 Angle : 0.607 9.330 9312 Z= 0.315 Chirality : 0.043 0.161 1127 Planarity : 0.005 0.062 1155 Dihedral : 4.772 59.969 957 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.72 % 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: 0.87 (0.28), residues: 874 helix: 1.70 (0.26), residues: 386 sheet: 0.18 (0.38), residues: 189 loop : -0.57 (0.36), residues: 299 *********************** 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 133 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.768 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 124 average time/residue: 0.9113 time to fit residues: 120.8985 Evaluate side-chains 106 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0628 time to fit residues: 1.1547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 340 ASN ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3039 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= 0.250 Angle : 0.545 10.852 9312 Z= 0.280 Chirality : 0.040 0.153 1127 Planarity : 0.004 0.055 1155 Dihedral : 4.670 57.456 957 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.28), residues: 874 helix: 1.67 (0.26), residues: 386 sheet: 0.08 (0.38), residues: 185 loop : -0.66 (0.35), residues: 303 *********************** 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 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.784 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 120 average time/residue: 0.8870 time to fit residues: 114.1243 Evaluate side-chains 104 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0843 time to fit residues: 1.3270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 41 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 75 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3117 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= 0.175 Angle : 0.514 9.780 9312 Z= 0.263 Chirality : 0.040 0.154 1127 Planarity : 0.003 0.050 1155 Dihedral : 4.442 56.759 957 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 874 helix: 1.70 (0.26), residues: 391 sheet: 0.05 (0.39), residues: 169 loop : -0.69 (0.35), residues: 314 *********************** 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 121 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.755 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.9148 time to fit residues: 110.6439 Evaluate side-chains 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.4213 time to fit residues: 3.4663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 28 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: ** 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: 0.7293 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6810 Z= 0.212 Angle : 0.542 12.608 9312 Z= 0.277 Chirality : 0.040 0.155 1127 Planarity : 0.004 0.047 1155 Dihedral : 4.586 55.994 957 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 4.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 874 helix: 1.81 (0.26), residues: 381 sheet: 0.06 (0.39), residues: 171 loop : -0.71 (0.35), residues: 322 *********************** 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 130 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.789 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 117 average time/residue: 0.8881 time to fit residues: 111.4016 Evaluate side-chains 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.0772 time to fit residues: 1.4259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 69 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6810 Z= 0.166 Angle : 0.524 13.064 9312 Z= 0.267 Chirality : 0.039 0.151 1127 Planarity : 0.003 0.045 1155 Dihedral : 4.441 55.905 957 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 874 helix: 1.80 (0.27), residues: 386 sheet: 0.03 (0.39), residues: 175 loop : -0.73 (0.35), residues: 313 *********************** 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 119 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.764 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 115 average time/residue: 0.8853 time to fit residues: 109.2402 Evaluate side-chains 103 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1118 time to fit residues: 1.2703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7271 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6810 Z= 0.179 Angle : 0.527 11.815 9312 Z= 0.271 Chirality : 0.039 0.149 1127 Planarity : 0.003 0.044 1155 Dihedral : 4.501 55.987 957 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 3.33 % 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: 0.83 (0.29), residues: 874 helix: 1.88 (0.27), residues: 382 sheet: -0.02 (0.38), residues: 175 loop : -0.71 (0.35), residues: 317 *********************** 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 116 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.793 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 0.8522 time to fit residues: 97.1303 Evaluate side-chains 106 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.3666 time to fit residues: 3.5520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.0270 chunk 41 optimal weight: 0.0670 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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: 0.7271 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6810 Z= 0.178 Angle : 0.536 11.602 9312 Z= 0.274 Chirality : 0.039 0.149 1127 Planarity : 0.003 0.043 1155 Dihedral : 4.521 56.297 957 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.57 % 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 (0.29), residues: 874 helix: 1.88 (0.26), residues: 382 sheet: -0.10 (0.39), residues: 169 loop : -0.71 (0.35), residues: 323 *********************** 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 106 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.807 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 101 average time/residue: 0.8982 time to fit residues: 97.3799 Evaluate side-chains 96 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1047 time to fit residues: 1.2360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 82 optimal weight: 0.0000 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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: 0.7280 moved from start: 0.3665 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= 0.188 Angle : 0.544 11.195 9312 Z= 0.278 Chirality : 0.040 0.148 1127 Planarity : 0.003 0.045 1155 Dihedral : 4.558 56.766 957 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 874 helix: 1.80 (0.26), residues: 389 sheet: -0.14 (0.39), residues: 169 loop : -0.71 (0.35), residues: 316 *********************** 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 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.779 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.9620 time to fit residues: 106.9763 Evaluate side-chains 104 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 1.6713 time to fit residues: 2.7976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3835 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= 0.223 Angle : 0.564 11.082 9312 Z= 0.290 Chirality : 0.040 0.146 1127 Planarity : 0.003 0.042 1155 Dihedral : 4.757 57.744 957 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.29), residues: 874 helix: 1.72 (0.26), residues: 390 sheet: -0.22 (0.39), residues: 168 loop : -0.76 (0.35), residues: 316 ********************** 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 111 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.845 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 107 average time/residue: 0.8723 time to fit residues: 100.6348 Evaluate side-chains 100 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.0791 time to fit residues: 1.5227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 0.0370 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124890 restraints weight = 6933.553| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.13 r_work: 0.3418 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3857 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= 0.198 Angle : 0.563 10.924 9312 Z= 0.289 Chirality : 0.040 0.147 1127 Planarity : 0.004 0.049 1155 Dihedral : 4.771 59.107 957 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.27 % 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 (0.29), residues: 874 helix: 1.71 (0.26), residues: 390 sheet: -0.21 (0.39), residues: 168 loop : -0.81 (0.35), residues: 316 =============================================================================== Job complete usr+sys time: 2947.78 seconds wall clock time: 52 minutes 51.45 seconds (3171.45 seconds total)