Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 11:37:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/08_2023/6ojq_20092_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/08_2023/6ojq_20092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/08_2023/6ojq_20092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/08_2023/6ojq_20092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/08_2023/6ojq_20092_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/08_2023/6ojq_20092_trim_updated.pdb" } resolution = 3.67 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2420 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 5760 2.51 5 N 1570 2.21 5 O 1784 1.98 5 H 8878 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 18055 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 6561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6561 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6597 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4831 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.11, per 1000 atoms: 0.45 Number of scatterers: 18055 At special positions: 0 Unit cell: (76.7, 106.6, 110.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 55 16.00 P 6 15.00 Mg 2 11.99 O 1784 8.00 N 1570 7.00 C 5760 6.00 H 8878 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.88 Conformation dependent library (CDL) restraints added in 1.9 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 10 sheets defined 42.4% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'B' and resid 11 through 28 Processing helix chain 'B' and resid 44 through 51 removed outlier: 3.653A pdb=" N ILE B 49 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ASN B 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 51 " --> pdb=" O ARG B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 51' Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 110 through 127 removed outlier: 4.754A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.132A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 383 through 399 removed outlier: 4.762A pdb=" N ILE B 391 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 415 through 434 Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.548A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.251A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 4.207A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.767A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.564A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.760A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 Processing helix chain 'K' and resid 20 through 23 No H-bonds generated for 'chain 'K' and resid 20 through 23' Processing helix chain 'K' and resid 58 through 65 Processing helix chain 'K' and resid 67 through 75 removed outlier: 4.050A pdb=" N GLU K 75 " --> pdb=" O LYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'K' and resid 108 through 121 removed outlier: 3.621A pdb=" N TYR K 120 " --> pdb=" O PHE K 116 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER K 121 " --> pdb=" O ASN K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 189 removed outlier: 4.033A pdb=" N ASN K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 241 No H-bonds generated for 'chain 'K' and resid 238 through 241' Processing helix chain 'K' and resid 246 through 269 Processing helix chain 'K' and resid 277 through 279 No H-bonds generated for 'chain 'K' and resid 277 through 279' Processing helix chain 'K' and resid 281 through 284 No H-bonds generated for 'chain 'K' and resid 281 through 284' Processing helix chain 'K' and resid 306 through 323 removed outlier: 5.373A pdb=" N SER K 310 " --> pdb=" O TYR K 307 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU K 311 " --> pdb=" O ASN K 308 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG K 321 " --> pdb=" O PHE K 318 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS K 323 " --> pdb=" O GLN K 320 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 136 through 138 Processing sheet with id= B, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'B' and resid 167 through 172 removed outlier: 6.944A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 269 through 273 removed outlier: 3.919A pdb=" N ALA B 273 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 6 through 9 Processing sheet with id= F, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.954A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.782A pdb=" N CYS A 376 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 318 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 316 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 50 through 52 removed outlier: 3.673A pdb=" N ARG K 50 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR K 296 " --> pdb=" O LYS K 10 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N MET K 12 " --> pdb=" O THR K 296 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE K 298 " --> pdb=" O MET K 12 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG K 14 " --> pdb=" O ILE K 298 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE K 300 " --> pdb=" O ARG K 14 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG K 16 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N CYS K 302 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE K 82 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N CYS K 301 " --> pdb=" O PHE K 82 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR K 84 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N SER K 303 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 32 through 34 Processing sheet with id= J, first strand: chain 'K' and resid 154 through 156 removed outlier: 4.389A pdb=" N SER K 154 " --> pdb=" O LYS K 166 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 945 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: 6.24 Time building geometry restraints manager: 15.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 8855 1.05 - 1.26: 1580 1.26 - 1.48: 3803 1.48 - 1.69: 3918 1.69 - 1.91: 90 Bond restraints: 18246 Sorted by residual: bond pdb=" C1' G2P B 501 " pdb=" C2' G2P B 501 " ideal model delta sigma weight residual 1.537 1.261 0.276 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 1.524 1.274 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3' G2P B 501 " pdb=" C4' G2P B 501 " ideal model delta sigma weight residual 1.526 1.282 0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " ideal model delta sigma weight residual 1.524 1.283 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1' G2P B 501 " pdb=" O4' G2P B 501 " ideal model delta sigma weight residual 1.389 1.558 -0.169 2.00e-02 2.50e+03 7.12e+01 ... (remaining 18241 not shown) Histogram of bond angle deviations from ideal: 99.50 - 108.03: 3531 108.03 - 116.56: 19986 116.56 - 125.08: 8873 125.08 - 133.61: 463 133.61 - 142.14: 10 Bond angle restraints: 32863 Sorted by residual: angle pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" C8 GTP A 501 " ideal model delta sigma weight residual 126.00 109.14 16.86 3.00e+00 1.11e-01 3.16e+01 angle pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" C4 GTP A 501 " ideal model delta sigma weight residual 126.00 142.14 -16.14 3.00e+00 1.11e-01 2.90e+01 angle pdb=" PA G2P B 501 " pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 120.83 108.79 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C4 G2P B 501 " ideal model delta sigma weight residual 125.17 113.59 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C8 G2P B 501 " ideal model delta sigma weight residual 127.92 138.20 -10.28 3.00e+00 1.11e-01 1.17e+01 ... (remaining 32858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 7301 35.32 - 70.63: 44 70.63 - 105.95: 2 105.95 - 141.26: 1 141.26 - 176.58: 3 Dihedral angle restraints: 7351 sinusoidal: 3390 harmonic: 3961 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -114.15 -176.58 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -47.08 151.67 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 125.64 148.48 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 7348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1082 0.050 - 0.099: 258 0.099 - 0.149: 53 0.149 - 0.199: 5 0.199 - 0.248: 2 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL A 182 " pdb=" CA VAL A 182 " pdb=" CG1 VAL A 182 " pdb=" CG2 VAL A 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 1397 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 269 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 270 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 214 " -0.015 2.00e-02 2.50e+03 1.04e-02 3.26e+00 pdb=" CG PHE B 214 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 214 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 214 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 214 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 214 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 214 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 214 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 214 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 214 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 214 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 214 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 387 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C LEU B 387 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU B 387 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE B 388 " -0.010 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 2034 2.25 - 2.84: 41161 2.84 - 3.43: 46431 3.43 - 4.01: 63959 4.01 - 4.60: 99754 Nonbonded interactions: 253339 Sorted by model distance: nonbonded pdb=" O TRP A 388 " pdb=" H ASP A 392 " model vdw 1.668 1.850 nonbonded pdb=" O ILE B 157 " pdb=" H TYR B 161 " model vdw 1.685 1.850 nonbonded pdb=" OG SER A 241 " pdb=" H VAL A 250 " model vdw 1.716 1.850 nonbonded pdb="HH22 ARG K 190 " pdb=" OD2 ASP K 231 " model vdw 1.723 1.850 nonbonded pdb=" HH TYR A 108 " pdb=" O ALA K 243 " model vdw 1.728 1.850 ... (remaining 253334 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.270 Extract box with map and model: 21.430 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 58.170 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.009 0.276 9368 Z= 0.589 Angle : 0.783 16.860 12701 Z= 0.394 Chirality : 0.045 0.248 1400 Planarity : 0.004 0.049 1650 Dihedral : 10.330 176.576 3438 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -3.02 (0.22), residues: 1154 helix: -1.03 (0.21), residues: 472 sheet: -3.13 (0.30), residues: 196 loop : -2.37 (0.27), residues: 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.6441 time to fit residues: 157.9150 Evaluate side-chains 81 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 192 HIS B 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 9368 Z= 0.322 Angle : 0.574 7.235 12701 Z= 0.299 Chirality : 0.042 0.183 1400 Planarity : 0.004 0.038 1650 Dihedral : 9.710 170.352 1281 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.12 (0.24), residues: 1154 helix: -0.07 (0.24), residues: 471 sheet: -2.76 (0.32), residues: 196 loop : -2.09 (0.29), residues: 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.5260 time to fit residues: 65.2137 Evaluate side-chains 73 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2210 time to fit residues: 5.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9368 Z= 0.263 Angle : 0.521 6.285 12701 Z= 0.269 Chirality : 0.041 0.141 1400 Planarity : 0.003 0.042 1650 Dihedral : 9.035 159.461 1281 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.73 (0.25), residues: 1154 helix: 0.33 (0.24), residues: 472 sheet: -2.57 (0.32), residues: 196 loop : -1.96 (0.29), residues: 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 72 average time/residue: 0.4948 time to fit residues: 50.4667 Evaluate side-chains 63 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2095 time to fit residues: 2.1778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS K 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 9368 Z= 0.185 Angle : 0.482 6.511 12701 Z= 0.245 Chirality : 0.040 0.142 1400 Planarity : 0.003 0.033 1650 Dihedral : 8.502 151.504 1281 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.34 (0.26), residues: 1154 helix: 0.67 (0.25), residues: 472 sheet: -2.32 (0.34), residues: 196 loop : -1.80 (0.29), residues: 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.4999 time to fit residues: 48.6048 Evaluate side-chains 62 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2624 time to fit residues: 2.5660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.0060 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9368 Z= 0.191 Angle : 0.473 5.751 12701 Z= 0.241 Chirality : 0.040 0.140 1400 Planarity : 0.003 0.029 1650 Dihedral : 8.199 148.141 1281 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.11 (0.26), residues: 1154 helix: 0.90 (0.25), residues: 471 sheet: -2.17 (0.34), residues: 201 loop : -1.70 (0.29), residues: 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.5190 time to fit residues: 45.1538 Evaluate side-chains 59 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1941 time to fit residues: 2.2344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9368 Z= 0.273 Angle : 0.508 6.564 12701 Z= 0.261 Chirality : 0.041 0.137 1400 Planarity : 0.003 0.029 1650 Dihedral : 8.180 144.327 1281 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.17 (0.26), residues: 1154 helix: 0.84 (0.25), residues: 473 sheet: -2.19 (0.34), residues: 201 loop : -1.74 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 0.4633 time to fit residues: 40.3295 Evaluate side-chains 58 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2321 time to fit residues: 2.6093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9368 Z= 0.184 Angle : 0.466 6.250 12701 Z= 0.238 Chirality : 0.040 0.141 1400 Planarity : 0.003 0.029 1650 Dihedral : 7.928 140.414 1281 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.98 (0.26), residues: 1154 helix: 1.03 (0.26), residues: 470 sheet: -2.12 (0.34), residues: 203 loop : -1.65 (0.29), residues: 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.4690 time to fit residues: 40.1099 Evaluate side-chains 58 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9368 Z= 0.207 Angle : 0.472 6.666 12701 Z= 0.241 Chirality : 0.040 0.139 1400 Planarity : 0.003 0.028 1650 Dihedral : 7.760 136.533 1281 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.92 (0.26), residues: 1154 helix: 1.09 (0.26), residues: 470 sheet: -2.07 (0.34), residues: 203 loop : -1.63 (0.29), residues: 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.604 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.4995 time to fit residues: 45.1489 Evaluate side-chains 60 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1841 time to fit residues: 2.1925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9368 Z= 0.263 Angle : 0.499 7.017 12701 Z= 0.256 Chirality : 0.041 0.137 1400 Planarity : 0.003 0.031 1650 Dihedral : 7.745 133.822 1281 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.04 (0.26), residues: 1154 helix: 0.97 (0.25), residues: 473 sheet: -2.11 (0.34), residues: 203 loop : -1.71 (0.29), residues: 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.4596 time to fit residues: 42.4935 Evaluate side-chains 61 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1865 time to fit residues: 1.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9368 Z= 0.236 Angle : 0.487 7.640 12701 Z= 0.249 Chirality : 0.041 0.139 1400 Planarity : 0.003 0.029 1650 Dihedral : 7.669 131.495 1281 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.93 (0.26), residues: 1154 helix: 1.04 (0.25), residues: 471 sheet: -2.06 (0.34), residues: 203 loop : -1.61 (0.29), residues: 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.4502 time to fit residues: 40.2620 Evaluate side-chains 59 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.099594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085845 restraints weight = 50359.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089384 restraints weight = 19375.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091413 restraints weight = 9687.508| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9368 Z= 0.184 Angle : 0.464 7.179 12701 Z= 0.237 Chirality : 0.040 0.140 1400 Planarity : 0.003 0.029 1650 Dihedral : 7.520 129.207 1281 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.26), residues: 1154 helix: 1.15 (0.25), residues: 468 sheet: -2.02 (0.34), residues: 204 loop : -1.54 (0.29), residues: 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3636.06 seconds wall clock time: 65 minutes 52.89 seconds (3952.89 seconds total)