Starting phenix.real_space_refine on Mon Mar 18 09:04:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/03_2024/6ojq_20092_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/03_2024/6ojq_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_20092/03_2024/6ojq_20092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/03_2024/6ojq_20092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/03_2024/6ojq_20092_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ojq_20092/03_2024/6ojq_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-dev-5265/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: 8.39, per 1000 atoms: 0.46 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: 15.30 Conformation dependent library (CDL) restraints added in 1.8 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: 2.95 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: 6.41 Time building geometry restraints manager: 15.79 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: 8491 35.32 - 70.63: 163 70.63 - 105.95: 2 105.95 - 141.26: 1 141.26 - 176.58: 3 Dihedral angle restraints: 8660 sinusoidal: 4699 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 8657 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: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.290 Extract box with map and model: 19.950 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 60.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.400 ------------------------------------------------------------------------------- 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 : 10.579 176.576 3466 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 % Allowed : 1.31 % Favored : 98.69 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 21 HIS 0.009 0.001 HIS A 8 PHE 0.031 0.002 PHE B 214 TYR 0.020 0.002 TYR A 432 ARG 0.011 0.001 ARG B 215 *********************** 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 : 1.621 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 REVERT: B 179 ASP cc_start: 0.7358 (t70) cc_final: 0.6945 (t0) REVERT: B 205 ASP cc_start: 0.7599 (t70) cc_final: 0.7336 (t0) REVERT: B 278 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8188 (mmt180) REVERT: B 305 CYS cc_start: 0.7910 (m) cc_final: 0.7689 (p) REVERT: A 101 ASN cc_start: 0.8670 (t160) cc_final: 0.8393 (t0) REVERT: A 290 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 302 MET cc_start: 0.8599 (mmp) cc_final: 0.8040 (mmp) REVERT: K 113 GLN cc_start: 0.7453 (mt0) cc_final: 0.6545 (pp30) REVERT: K 185 GLU cc_start: 0.8790 (tt0) cc_final: 0.8406 (tm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.6398 time to fit residues: 157.3360 Evaluate side-chains 87 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9368 Z= 0.187 Angle : 0.503 6.596 12701 Z= 0.259 Chirality : 0.040 0.143 1400 Planarity : 0.004 0.043 1650 Dihedral : 10.341 173.389 1309 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.91 % Allowed : 4.73 % Favored : 94.37 % 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: -1.98 (0.24), residues: 1154 helix: 0.04 (0.24), residues: 471 sheet: -2.63 (0.32), residues: 198 loop : -2.02 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 PHE 0.012 0.001 PHE A 255 TYR 0.008 0.001 TYR A 224 ARG 0.003 0.000 ARG K 50 *********************** 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 97 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.563 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 revert: symmetry clash REVERT: B 179 ASP cc_start: 0.7477 (t70) cc_final: 0.7055 (t0) REVERT: B 205 ASP cc_start: 0.7850 (t70) cc_final: 0.7564 (t0) REVERT: B 278 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8179 (mmt180) REVERT: A 290 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8043 (tt0) REVERT: K 185 GLU cc_start: 0.8615 (tt0) cc_final: 0.8401 (tm-30) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.4872 time to fit residues: 66.2984 Evaluate side-chains 85 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 239 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9368 Z= 0.263 Angle : 0.517 6.181 12701 Z= 0.268 Chirality : 0.041 0.138 1400 Planarity : 0.004 0.047 1650 Dihedral : 9.622 160.227 1309 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.21 % Allowed : 5.23 % Favored : 93.56 % 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: -1.57 (0.25), residues: 1154 helix: 0.43 (0.24), residues: 473 sheet: -2.42 (0.33), residues: 194 loop : -1.88 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.006 0.001 HIS A 8 PHE 0.014 0.001 PHE A 255 TYR 0.009 0.001 TYR A 24 ARG 0.006 0.000 ARG A 339 *********************** 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 88 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.121 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: B 33 THR cc_start: 0.9051 (p) cc_final: 0.8810 (t) REVERT: B 179 ASP cc_start: 0.7710 (t70) cc_final: 0.7293 (t0) REVERT: B 278 ARG cc_start: 0.8426 (mmm160) cc_final: 0.8123 (mmt180) REVERT: B 415 GLU cc_start: 0.6156 (tm-30) cc_final: 0.5854 (tm-30) REVERT: A 290 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7964 (tt0) REVERT: K 220 GLU cc_start: 0.7530 (mp0) cc_final: 0.7150 (mp0) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.4955 time to fit residues: 59.6493 Evaluate side-chains 78 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 0.0060 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS K 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9368 Z= 0.235 Angle : 0.492 6.138 12701 Z= 0.253 Chirality : 0.040 0.140 1400 Planarity : 0.003 0.042 1650 Dihedral : 9.217 149.631 1309 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.11 % Allowed : 5.53 % Favored : 93.36 % 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: -1.31 (0.25), residues: 1154 helix: 0.70 (0.25), residues: 471 sheet: -2.26 (0.34), residues: 196 loop : -1.80 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.006 0.001 HIS A 8 PHE 0.009 0.001 PHE K 208 TYR 0.008 0.001 TYR K 277 ARG 0.003 0.000 ARG A 339 *********************** 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 86 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.465 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: B 33 THR cc_start: 0.9129 (p) cc_final: 0.8890 (t) REVERT: B 179 ASP cc_start: 0.7745 (t70) cc_final: 0.7290 (t0) REVERT: B 278 ARG cc_start: 0.8416 (mmm160) cc_final: 0.8126 (mmt180) REVERT: B 323 MET cc_start: 0.8190 (mtt) cc_final: 0.7327 (mtt) REVERT: B 415 GLU cc_start: 0.6242 (tm-30) cc_final: 0.5801 (tm-30) REVERT: A 290 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7976 (tt0) REVERT: K 50 ARG cc_start: 0.7667 (mmm160) cc_final: 0.6846 (tpt90) REVERT: K 220 GLU cc_start: 0.7625 (mp0) cc_final: 0.7308 (mp0) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.5063 time to fit residues: 60.5711 Evaluate side-chains 80 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9368 Z= 0.219 Angle : 0.484 6.399 12701 Z= 0.248 Chirality : 0.040 0.138 1400 Planarity : 0.003 0.036 1650 Dihedral : 9.041 146.718 1309 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.41 % Allowed : 6.34 % Favored : 92.25 % 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: 0.83 (0.25), residues: 471 sheet: -2.23 (0.34), residues: 203 loop : -1.69 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 PHE 0.022 0.001 PHE B 169 TYR 0.007 0.001 TYR K 277 ARG 0.002 0.000 ARG A 156 *********************** 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 83 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.491 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: B 33 THR cc_start: 0.9154 (p) cc_final: 0.8914 (t) REVERT: B 179 ASP cc_start: 0.7723 (t70) cc_final: 0.7288 (t0) REVERT: B 278 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8136 (mmt180) REVERT: B 415 GLU cc_start: 0.6268 (tm-30) cc_final: 0.5834 (tm-30) REVERT: A 290 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7967 (tt0) REVERT: K 50 ARG cc_start: 0.7688 (mmm160) cc_final: 0.6868 (tpt90) REVERT: K 220 GLU cc_start: 0.7618 (mp0) cc_final: 0.7207 (mp0) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.5088 time to fit residues: 58.2020 Evaluate side-chains 79 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 ASN A 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9368 Z= 0.353 Angle : 0.547 6.484 12701 Z= 0.285 Chirality : 0.042 0.142 1400 Planarity : 0.004 0.036 1650 Dihedral : 9.215 141.589 1309 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.61 % Allowed : 6.44 % Favored : 91.95 % 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: -1.38 (0.25), residues: 1154 helix: 0.64 (0.25), residues: 473 sheet: -2.34 (0.34), residues: 203 loop : -1.79 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 388 HIS 0.006 0.001 HIS A 8 PHE 0.020 0.002 PHE B 169 TYR 0.010 0.001 TYR K 134 ARG 0.004 0.001 ARG A 121 *********************** 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 83 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.9187 (p) cc_final: 0.8954 (t) REVERT: B 179 ASP cc_start: 0.7774 (t70) cc_final: 0.7338 (t0) REVERT: B 278 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8110 (mmt180) REVERT: B 415 GLU cc_start: 0.6461 (tm-30) cc_final: 0.6209 (tm-30) REVERT: A 290 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7952 (tt0) REVERT: K 50 ARG cc_start: 0.7744 (mmm160) cc_final: 0.6892 (tpt90) outliers start: 16 outliers final: 15 residues processed: 83 average time/residue: 0.4681 time to fit residues: 54.9554 Evaluate side-chains 81 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3847 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= 0.181 Angle : 0.472 6.675 12701 Z= 0.241 Chirality : 0.040 0.142 1400 Planarity : 0.003 0.031 1650 Dihedral : 8.882 137.485 1309 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.01 % Allowed : 7.24 % Favored : 91.75 % 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: -1.05 (0.26), residues: 1154 helix: 0.96 (0.25), residues: 469 sheet: -2.27 (0.34), residues: 206 loop : -1.59 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS A 8 PHE 0.012 0.001 PHE B 169 TYR 0.008 0.001 TYR K 118 ARG 0.002 0.000 ARG A 264 *********************** 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 82 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.9192 (p) cc_final: 0.8956 (t) REVERT: B 179 ASP cc_start: 0.7800 (t70) cc_final: 0.7327 (t0) REVERT: B 278 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8113 (mmt180) REVERT: B 415 GLU cc_start: 0.6386 (tm-30) cc_final: 0.5919 (tm-30) REVERT: B 416 MET cc_start: 0.7999 (tpp) cc_final: 0.7783 (tpp) REVERT: A 290 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7934 (tt0) REVERT: A 417 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: K 50 ARG cc_start: 0.7729 (mmm160) cc_final: 0.6896 (tpt90) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.5120 time to fit residues: 58.0067 Evaluate side-chains 77 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7478 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9368 Z= 0.228 Angle : 0.480 5.935 12701 Z= 0.246 Chirality : 0.040 0.139 1400 Planarity : 0.003 0.051 1650 Dihedral : 8.763 135.556 1309 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.41 % Allowed : 6.94 % Favored : 91.65 % 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: -1.02 (0.26), residues: 1154 helix: 0.97 (0.25), residues: 469 sheet: -2.21 (0.34), residues: 206 loop : -1.59 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 8 PHE 0.015 0.001 PHE B 169 TYR 0.008 0.001 TYR K 274 ARG 0.004 0.000 ARG A 264 *********************** 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 81 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.9190 (p) cc_final: 0.8957 (t) REVERT: B 179 ASP cc_start: 0.7797 (t70) cc_final: 0.7312 (t0) REVERT: B 278 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8096 (mmt180) REVERT: B 415 GLU cc_start: 0.6433 (tm-30) cc_final: 0.5963 (tm-30) REVERT: B 416 MET cc_start: 0.7980 (tpp) cc_final: 0.7736 (tpp) REVERT: A 203 MET cc_start: 0.8904 (mmm) cc_final: 0.8628 (mtp) REVERT: A 290 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7932 (tt0) REVERT: A 417 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: K 50 ARG cc_start: 0.7745 (mmm160) cc_final: 0.6908 (tpt90) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.4784 time to fit residues: 54.9271 Evaluate side-chains 79 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 97 optimal weight: 0.0010 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- 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: 0.4105 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= 0.220 Angle : 0.473 5.720 12701 Z= 0.243 Chirality : 0.040 0.138 1400 Planarity : 0.003 0.032 1650 Dihedral : 8.591 130.823 1309 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.21 % Allowed : 7.14 % Favored : 91.65 % 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: -0.96 (0.26), residues: 1154 helix: 1.00 (0.25), residues: 469 sheet: -2.15 (0.34), residues: 206 loop : -1.55 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 8 PHE 0.013 0.001 PHE B 169 TYR 0.008 0.001 TYR K 134 ARG 0.002 0.000 ARG A 215 *********************** 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 80 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.9196 (p) cc_final: 0.8966 (t) REVERT: B 179 ASP cc_start: 0.7737 (t70) cc_final: 0.7246 (t0) REVERT: B 278 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8120 (mmt180) REVERT: A 290 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7883 (tt0) REVERT: A 417 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: K 50 ARG cc_start: 0.7764 (mmm160) cc_final: 0.6921 (tpt90) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.4812 time to fit residues: 55.0618 Evaluate side-chains 77 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9368 Z= 0.200 Angle : 0.462 5.623 12701 Z= 0.237 Chirality : 0.040 0.138 1400 Planarity : 0.003 0.032 1650 Dihedral : 8.479 128.727 1309 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.31 % Allowed : 7.14 % Favored : 91.55 % 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: -0.91 (0.26), residues: 1154 helix: 1.07 (0.25), residues: 467 sheet: -2.15 (0.34), residues: 209 loop : -1.52 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 8 PHE 0.013 0.001 PHE B 169 TYR 0.009 0.001 TYR K 134 ARG 0.002 0.000 ARG A 215 ********************** 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 78 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.9203 (p) cc_final: 0.8967 (t) REVERT: B 179 ASP cc_start: 0.7742 (t70) cc_final: 0.7243 (t0) REVERT: B 278 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8151 (mmt180) REVERT: A 290 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7884 (tt0) REVERT: A 417 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: K 50 ARG cc_start: 0.7787 (mmm160) cc_final: 0.6938 (tpt90) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.4397 time to fit residues: 48.6085 Evaluate side-chains 78 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 253 ASN Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.097500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083885 restraints weight = 50636.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087410 restraints weight = 19543.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089468 restraints weight = 9765.123| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9368 Z= 0.256 Angle : 0.484 5.703 12701 Z= 0.250 Chirality : 0.041 0.136 1400 Planarity : 0.003 0.034 1650 Dihedral : 8.524 128.074 1309 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.51 % Allowed : 6.74 % Favored : 91.75 % 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: -1.00 (0.26), residues: 1154 helix: 0.96 (0.25), residues: 472 sheet: -2.15 (0.34), residues: 206 loop : -1.59 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 PHE 0.015 0.001 PHE B 169 TYR 0.010 0.001 TYR K 134 ARG 0.002 0.000 ARG A 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3765.55 seconds wall clock time: 69 minutes 16.14 seconds (4156.14 seconds total)