Starting phenix.real_space_refine on Thu Feb 15 07:50:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5r_12048/02_2024/7b5r_12048_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5r_12048/02_2024/7b5r_12048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5r_12048/02_2024/7b5r_12048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5r_12048/02_2024/7b5r_12048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5r_12048/02_2024/7b5r_12048_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5r_12048/02_2024/7b5r_12048_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 53 5.16 5 C 7437 2.51 5 N 1966 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "T PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 283": "OE1" <-> "OE2" Residue "T GLU 358": "OE1" <-> "OE2" Residue "K ASP 10": "OD1" <-> "OD2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 27": "OD1" <-> "OD2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "S PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 208": "OE1" <-> "OE2" Residue "Y TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 220": "OE1" <-> "OE2" Residue "Y GLU 230": "OE1" <-> "OE2" Residue "Y GLU 274": "OE1" <-> "OE2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "P GLU 39": "OE1" <-> "OE2" Residue "P PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11606 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2396 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2536 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "S" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2279 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2046 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Chain: "P" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 654 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.28, per 1000 atoms: 0.54 Number of scatterers: 11606 At special positions: 0 Unit cell: (149.33, 126.44, 103.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 2 15.00 O 2148 8.00 N 1966 7.00 C 7437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 2.1 seconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 6 sheets defined 48.7% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.216A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 86 through 105 Processing helix chain 'C' and resid 115 through 136 removed outlier: 4.283A pdb=" N GLN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 174 through 190 removed outlier: 4.037A pdb=" N VAL C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.412A pdb=" N SER C 202 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY C 203 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 233 through 254 removed outlier: 3.527A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 278 removed outlier: 4.140A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN C 276 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'T' and resid 97 through 99 No H-bonds generated for 'chain 'T' and resid 97 through 99' Processing helix chain 'T' and resid 102 through 111 removed outlier: 4.213A pdb=" N CYS T 111 " --> pdb=" O GLY T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 121 Processing helix chain 'T' and resid 125 through 130 Processing helix chain 'T' and resid 149 through 157 Processing helix chain 'T' and resid 195 through 202 Processing helix chain 'T' and resid 220 through 228 removed outlier: 4.227A pdb=" N LYS T 228 " --> pdb=" O ASN T 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 245 through 254 Processing helix chain 'T' and resid 271 through 280 Processing helix chain 'T' and resid 299 through 308 Processing helix chain 'T' and resid 325 through 333 Processing helix chain 'T' and resid 351 through 358 removed outlier: 3.553A pdb=" N GLY T 357 " --> pdb=" O LEU T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 375 through 382 Processing helix chain 'T' and resid 409 through 411 No H-bonds generated for 'chain 'T' and resid 409 through 411' Processing helix chain 'K' and resid 26 through 31 removed outlier: 4.082A pdb=" N LEU K 31 " --> pdb=" O ASP K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'S' and resid 18 through 23 removed outlier: 4.428A pdb=" N GLN S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 32 Processing helix chain 'S' and resid 46 through 58 removed outlier: 3.814A pdb=" N LYS S 51 " --> pdb=" O ALA S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 92 Processing helix chain 'S' and resid 97 through 110 Processing helix chain 'S' and resid 113 through 127 Processing helix chain 'S' and resid 132 through 138 Processing helix chain 'S' and resid 150 through 157 removed outlier: 3.645A pdb=" N ASN S 157 " --> pdb=" O VAL S 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 55 Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 101 through 120 Processing helix chain 'L' and resid 130 through 132 No H-bonds generated for 'chain 'L' and resid 130 through 132' Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 171 through 174 No H-bonds generated for 'chain 'L' and resid 171 through 174' Processing helix chain 'L' and resid 184 through 198 Processing helix chain 'L' and resid 208 through 219 Processing helix chain 'L' and resid 248 through 252 removed outlier: 3.572A pdb=" N VAL L 252 " --> pdb=" O PHE L 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 248 through 252' Processing helix chain 'L' and resid 257 through 264 Processing helix chain 'L' and resid 277 through 282 removed outlier: 3.893A pdb=" N ALA L 282 " --> pdb=" O LYS L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 287 No H-bonds generated for 'chain 'L' and resid 284 through 287' Processing helix chain 'Y' and resid 179 through 191 removed outlier: 4.448A pdb=" N VAL Y 191 " --> pdb=" O ARG Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 198 through 202 removed outlier: 3.670A pdb=" N LYS Y 201 " --> pdb=" O GLY Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 224 Processing helix chain 'Y' and resid 229 through 245 removed outlier: 3.684A pdb=" N SER Y 245 " --> pdb=" O ARG Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 268 removed outlier: 3.562A pdb=" N LEU Y 253 " --> pdb=" O ARG Y 250 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN Y 254 " --> pdb=" O GLY Y 251 " (cutoff:3.500A) Processing helix chain 'Y' and resid 275 through 281 Processing helix chain 'Y' and resid 288 through 302 Processing helix chain 'Y' and resid 311 through 320 removed outlier: 3.909A pdb=" N LEU Y 320 " --> pdb=" O THR Y 316 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 342 Processing helix chain 'Y' and resid 352 through 368 Processing helix chain 'Y' and resid 374 through 380 Processing helix chain 'Y' and resid 388 through 401 Processing helix chain 'Y' and resid 408 through 413 Processing helix chain 'Y' and resid 416 through 418 No H-bonds generated for 'chain 'Y' and resid 416 through 418' Processing helix chain 'Y' and resid 421 through 423 No H-bonds generated for 'chain 'Y' and resid 421 through 423' Processing helix chain 'P' and resid 39 through 49 Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'P' and resid 86 through 89 Processing sheet with id= A, first strand: chain 'T' and resid 139 through 141 removed outlier: 6.197A pdb=" N ALA T 162 " --> pdb=" O LEU T 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'T' and resid 260 through 262 removed outlier: 6.051A pdb=" N GLN T 287 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS T 314 " --> pdb=" O LEU T 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 339 through 341 removed outlier: 6.041A pdb=" N THR T 364 " --> pdb=" O LEU T 340 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'K' and resid 17 through 23 Processing sheet with id= E, first strand: chain 'S' and resid 3 through 6 removed outlier: 3.510A pdb=" N LEU S 6 " --> pdb=" O PHE S 14 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 31 through 36 removed outlier: 3.702A pdb=" N ALA L 31 " --> pdb=" O PHE L 80 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3735 1.34 - 1.46: 1868 1.46 - 1.57: 6170 1.57 - 1.69: 6 1.69 - 1.81: 78 Bond restraints: 11857 Sorted by residual: bond pdb=" OG1 TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.717 1.615 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O1P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O2P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3P TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.27: 310 106.27 - 113.21: 6552 113.21 - 120.14: 4313 120.14 - 127.08: 4740 127.08 - 134.02: 141 Bond angle restraints: 16056 Sorted by residual: angle pdb=" N PRO S 2 " pdb=" CA PRO S 2 " pdb=" CB PRO S 2 " ideal model delta sigma weight residual 103.00 110.53 -7.53 1.10e+00 8.26e-01 4.68e+01 angle pdb=" CB TPO P 187 " pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 119.31 107.26 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N VAL L 164 " pdb=" CA VAL L 164 " pdb=" C VAL L 164 " ideal model delta sigma weight residual 109.34 116.61 -7.27 2.08e+00 2.31e-01 1.22e+01 angle pdb=" N GLY P 72 " pdb=" CA GLY P 72 " pdb=" C GLY P 72 " ideal model delta sigma weight residual 110.29 114.61 -4.32 1.28e+00 6.10e-01 1.14e+01 angle pdb=" CB TPO L 160 " pdb=" OG1 TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 119.31 109.24 10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 16051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6410 17.91 - 35.81: 639 35.81 - 53.72: 85 53.72 - 71.63: 23 71.63 - 89.54: 10 Dihedral angle restraints: 7167 sinusoidal: 2956 harmonic: 4211 Sorted by residual: dihedral pdb=" CA LEU K 37 " pdb=" C LEU K 37 " pdb=" N MET K 38 " pdb=" CA MET K 38 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA VAL L 163 " pdb=" C VAL L 163 " pdb=" N VAL L 164 " pdb=" CA VAL L 164 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ARG P 50 " pdb=" C ARG P 50 " pdb=" N ASP P 51 " pdb=" CA ASP P 51 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 7164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1317 0.047 - 0.094: 400 0.094 - 0.141: 80 0.141 - 0.188: 9 0.188 - 0.235: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA PRO S 2 " pdb=" N PRO S 2 " pdb=" C PRO S 2 " pdb=" CB PRO S 2 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL L 163 " pdb=" N VAL L 163 " pdb=" C VAL L 163 " pdb=" CB VAL L 163 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA PRO L 238 " pdb=" N PRO L 238 " pdb=" C PRO L 238 " pdb=" CB PRO L 238 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 1804 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 32 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO K 33 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO K 33 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 33 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 217 " 0.015 2.00e-02 2.50e+03 1.53e-02 5.88e+00 pdb=" CG TRP Y 217 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 217 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 217 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 217 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 217 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 217 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 217 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 217 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 217 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR S 131 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO S 132 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 132 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 132 " -0.031 5.00e-02 4.00e+02 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 149 2.58 - 3.16: 10795 3.16 - 3.74: 18171 3.74 - 4.32: 24287 4.32 - 4.90: 38843 Nonbonded interactions: 92245 Sorted by model distance: nonbonded pdb=" OD1 ASP Y 216 " pdb=" OG SER Y 408 " model vdw 2.001 2.440 nonbonded pdb=" O GLY Y 337 " pdb=" OG SER Y 340 " model vdw 2.109 2.440 nonbonded pdb=" OE2 GLU L 57 " pdb=" OH TYR Y 185 " model vdw 2.147 2.440 nonbonded pdb=" OH TYR Y 350 " pdb=" OD2 ASP Y 393 " model vdw 2.171 2.440 nonbonded pdb=" NH1 ARG L 157 " pdb=" OE2 GLU Y 268 " model vdw 2.171 2.520 ... (remaining 92240 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.060 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.070 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.006 0.114 11857 Z= 0.392 Angle : 0.806 12.049 16056 Z= 0.440 Chirality : 0.046 0.235 1807 Planarity : 0.005 0.064 2034 Dihedral : 14.425 89.536 4427 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1392 helix: 0.48 (0.19), residues: 734 sheet: -3.59 (0.53), residues: 80 loop : -2.45 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP Y 217 HIS 0.008 0.002 HIS K 56 PHE 0.020 0.002 PHE S 101 TYR 0.021 0.002 TYR Y 225 ARG 0.012 0.001 ARG P 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: C 301 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8734 (pm20) REVERT: K 14 ASP cc_start: 0.7886 (p0) cc_final: 0.7486 (p0) REVERT: K 54 TRP cc_start: 0.8759 (m100) cc_final: 0.7721 (m100) REVERT: Y 211 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.7890 (ttp80) REVERT: Y 250 ARG cc_start: 0.6697 (tpt170) cc_final: 0.6456 (tpt170) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2398 time to fit residues: 42.5648 Evaluate side-chains 86 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 177 HIS ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 HIS L 268 HIS Y 208 ASN ** Y 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11857 Z= 0.221 Angle : 0.612 10.090 16056 Z= 0.312 Chirality : 0.041 0.154 1807 Planarity : 0.005 0.055 2034 Dihedral : 5.228 38.878 1545 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.54 % Allowed : 7.53 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1392 helix: 0.63 (0.20), residues: 733 sheet: -3.41 (0.53), residues: 80 loop : -2.30 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Y 217 HIS 0.011 0.001 HIS T 177 PHE 0.015 0.002 PHE S 101 TYR 0.024 0.001 TYR L 180 ARG 0.003 0.000 ARG T 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 MET cc_start: 0.7752 (mmm) cc_final: 0.6918 (mmm) REVERT: T 121 SER cc_start: 0.9284 (t) cc_final: 0.9065 (p) REVERT: K 14 ASP cc_start: 0.7744 (p0) cc_final: 0.7356 (p0) REVERT: K 54 TRP cc_start: 0.8702 (m100) cc_final: 0.7900 (m100) REVERT: L 91 MET cc_start: 0.8458 (mtm) cc_final: 0.7999 (mtm) REVERT: Y 211 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.7919 (ttp80) REVERT: Y 328 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8542 (ptpt) REVERT: Y 371 SER cc_start: 0.7363 (m) cc_final: 0.7153 (t) outliers start: 7 outliers final: 6 residues processed: 103 average time/residue: 0.2299 time to fit residues: 34.9657 Evaluate side-chains 95 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 0.0470 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 136 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS Y 254 GLN ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11857 Z= 0.149 Angle : 0.540 10.788 16056 Z= 0.274 Chirality : 0.039 0.129 1807 Planarity : 0.004 0.054 2034 Dihedral : 4.765 38.792 1545 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.24 % Allowed : 9.54 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1392 helix: 0.83 (0.20), residues: 729 sheet: -2.55 (0.53), residues: 96 loop : -2.07 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 217 HIS 0.003 0.001 HIS Y 296 PHE 0.016 0.001 PHE T 328 TYR 0.021 0.001 TYR L 180 ARG 0.003 0.000 ARG T 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7966 (tmm) cc_final: 0.7669 (tmm) REVERT: T 121 SER cc_start: 0.9253 (t) cc_final: 0.9019 (p) REVERT: K 14 ASP cc_start: 0.7484 (p0) cc_final: 0.7012 (p0) REVERT: K 54 TRP cc_start: 0.8596 (m100) cc_final: 0.8049 (m100) REVERT: S 111 ASP cc_start: 0.8509 (t0) cc_final: 0.8033 (t70) REVERT: Y 211 ARG cc_start: 0.8538 (ptm-80) cc_final: 0.8333 (ttp80) REVERT: Y 293 ARG cc_start: 0.8669 (mmm160) cc_final: 0.8130 (mmm160) REVERT: Y 328 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8580 (mttm) REVERT: Y 371 SER cc_start: 0.7378 (m) cc_final: 0.7123 (t) REVERT: P 68 LYS cc_start: 0.8856 (tppt) cc_final: 0.8647 (tppt) outliers start: 16 outliers final: 10 residues processed: 114 average time/residue: 0.2384 time to fit residues: 40.2139 Evaluate side-chains 99 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 0.0030 chunk 126 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 177 HIS ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11857 Z= 0.161 Angle : 0.538 11.339 16056 Z= 0.270 Chirality : 0.039 0.136 1807 Planarity : 0.004 0.051 2034 Dihedral : 4.579 36.144 1545 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.78 % Allowed : 12.41 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1392 helix: 0.91 (0.20), residues: 729 sheet: -1.98 (0.61), residues: 82 loop : -2.10 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 43 HIS 0.003 0.001 HIS P 48 PHE 0.017 0.001 PHE T 328 TYR 0.020 0.001 TYR L 180 ARG 0.002 0.000 ARG T 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 121 SER cc_start: 0.9228 (t) cc_final: 0.8993 (p) REVERT: K 14 ASP cc_start: 0.7589 (p0) cc_final: 0.7177 (p0) REVERT: K 54 TRP cc_start: 0.8622 (m100) cc_final: 0.8318 (m100) REVERT: S 111 ASP cc_start: 0.8554 (t0) cc_final: 0.8039 (t70) REVERT: L 91 MET cc_start: 0.8562 (mtm) cc_final: 0.8258 (mtm) REVERT: Y 328 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8489 (ptpp) REVERT: Y 371 SER cc_start: 0.7450 (m) cc_final: 0.7172 (t) REVERT: P 39 GLU cc_start: 0.6725 (pm20) cc_final: 0.6509 (pp20) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 0.2449 time to fit residues: 40.9108 Evaluate side-chains 104 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain Y residue 254 GLN Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN T 177 HIS ** T 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 158 GLN L 119 HIS L 246 GLN ** Y 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11857 Z= 0.291 Angle : 0.619 11.959 16056 Z= 0.310 Chirality : 0.041 0.164 1807 Planarity : 0.005 0.049 2034 Dihedral : 4.843 28.553 1545 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.33 % Allowed : 14.12 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1392 helix: 0.82 (0.20), residues: 730 sheet: -2.22 (0.57), residues: 91 loop : -2.13 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 43 HIS 0.006 0.001 HIS T 177 PHE 0.020 0.002 PHE T 169 TYR 0.020 0.001 TYR L 180 ARG 0.006 0.000 ARG P 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7896 (tmm) cc_final: 0.7598 (tmm) REVERT: K 14 ASP cc_start: 0.7754 (p0) cc_final: 0.7217 (p0) REVERT: K 54 TRP cc_start: 0.8804 (m100) cc_final: 0.8513 (m100) REVERT: S 111 ASP cc_start: 0.8589 (t0) cc_final: 0.8090 (t70) REVERT: Y 293 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8316 (mmm160) REVERT: Y 371 SER cc_start: 0.7297 (m) cc_final: 0.7056 (t) outliers start: 30 outliers final: 20 residues processed: 112 average time/residue: 0.2337 time to fit residues: 38.6232 Evaluate side-chains 104 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 195 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain Y residue 254 GLN Chi-restraints excluded: chain P residue 51 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 134 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 GLN Y 179 HIS Y 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11857 Z= 0.153 Angle : 0.555 12.674 16056 Z= 0.273 Chirality : 0.039 0.134 1807 Planarity : 0.004 0.053 2034 Dihedral : 4.536 30.183 1545 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.94 % Allowed : 15.21 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.24), residues: 1392 helix: 0.97 (0.20), residues: 726 sheet: -2.38 (0.56), residues: 97 loop : -1.88 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 217 HIS 0.004 0.001 HIS P 48 PHE 0.021 0.001 PHE T 328 TYR 0.018 0.001 TYR L 180 ARG 0.005 0.000 ARG P 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7988 (tmm) cc_final: 0.7682 (tmm) REVERT: C 338 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7764 (ptmm) REVERT: K 14 ASP cc_start: 0.7483 (p0) cc_final: 0.6988 (p0) REVERT: S 111 ASP cc_start: 0.8473 (t0) cc_final: 0.7903 (t70) REVERT: L 91 MET cc_start: 0.8536 (mtm) cc_final: 0.8277 (mtm) REVERT: Y 293 ARG cc_start: 0.8747 (mmm160) cc_final: 0.8356 (mmm160) REVERT: Y 328 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8517 (ptpp) REVERT: Y 371 SER cc_start: 0.7313 (m) cc_final: 0.7079 (t) outliers start: 25 outliers final: 17 residues processed: 122 average time/residue: 0.2305 time to fit residues: 41.3974 Evaluate side-chains 114 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Chi-restraints excluded: chain Y residue 396 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 133 optimal weight: 0.0070 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11857 Z= 0.159 Angle : 0.547 12.572 16056 Z= 0.272 Chirality : 0.039 0.136 1807 Planarity : 0.004 0.051 2034 Dihedral : 4.433 29.264 1545 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.09 % Allowed : 15.59 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1392 helix: 1.11 (0.20), residues: 723 sheet: -2.32 (0.56), residues: 97 loop : -1.87 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 54 HIS 0.005 0.001 HIS Y 395 PHE 0.022 0.001 PHE T 328 TYR 0.018 0.001 TYR L 180 ARG 0.006 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7938 (tmm) cc_final: 0.7619 (tmm) REVERT: C 338 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7816 (ptmm) REVERT: K 14 ASP cc_start: 0.7505 (p0) cc_final: 0.7012 (p0) REVERT: S 111 ASP cc_start: 0.8462 (t0) cc_final: 0.7923 (t70) REVERT: L 233 MET cc_start: 0.9406 (mmt) cc_final: 0.9088 (mmt) REVERT: L 296 LEU cc_start: 0.1734 (OUTLIER) cc_final: 0.0784 (tp) REVERT: Y 293 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8505 (mmm160) REVERT: Y 328 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8486 (ptpp) REVERT: Y 371 SER cc_start: 0.7403 (m) cc_final: 0.7148 (t) outliers start: 27 outliers final: 20 residues processed: 119 average time/residue: 0.2174 time to fit residues: 38.5882 Evaluate side-chains 116 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 171 ASP Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 254 GLN Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Chi-restraints excluded: chain Y residue 396 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.0020 chunk 121 optimal weight: 3.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 396 GLN P 66 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11857 Z= 0.142 Angle : 0.552 12.404 16056 Z= 0.272 Chirality : 0.039 0.140 1807 Planarity : 0.004 0.054 2034 Dihedral : 4.281 30.394 1545 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.63 % Allowed : 16.14 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1392 helix: 1.17 (0.20), residues: 714 sheet: -2.18 (0.56), residues: 97 loop : -1.66 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 54 HIS 0.007 0.001 HIS Y 395 PHE 0.022 0.001 PHE T 328 TYR 0.017 0.001 TYR L 180 ARG 0.007 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8087 (tmm) cc_final: 0.7767 (tmm) REVERT: C 338 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7932 (ptmm) REVERT: K 14 ASP cc_start: 0.7438 (p0) cc_final: 0.6972 (p0) REVERT: S 110 LEU cc_start: 0.8864 (tp) cc_final: 0.8540 (tp) REVERT: S 111 ASP cc_start: 0.8379 (t0) cc_final: 0.7837 (t70) REVERT: L 91 MET cc_start: 0.8517 (mtm) cc_final: 0.8211 (mtm) REVERT: L 233 MET cc_start: 0.9392 (mmt) cc_final: 0.9181 (mmt) REVERT: L 296 LEU cc_start: 0.1557 (OUTLIER) cc_final: 0.0614 (tp) REVERT: Y 328 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8479 (ptpp) REVERT: Y 371 SER cc_start: 0.7337 (m) cc_final: 0.7081 (t) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.2141 time to fit residues: 36.4577 Evaluate side-chains 115 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Chi-restraints excluded: chain Y residue 396 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.0070 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11857 Z= 0.166 Angle : 0.565 12.353 16056 Z= 0.279 Chirality : 0.039 0.169 1807 Planarity : 0.004 0.051 2034 Dihedral : 4.261 29.206 1545 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.78 % Allowed : 16.60 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1392 helix: 1.21 (0.20), residues: 714 sheet: -1.72 (0.62), residues: 82 loop : -1.74 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 54 HIS 0.009 0.001 HIS Y 395 PHE 0.022 0.001 PHE T 328 TYR 0.017 0.001 TYR L 180 ARG 0.005 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8032 (tmm) cc_final: 0.7719 (tmm) REVERT: C 338 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7996 (ptmm) REVERT: K 14 ASP cc_start: 0.7496 (p0) cc_final: 0.7017 (p0) REVERT: S 110 LEU cc_start: 0.8905 (tp) cc_final: 0.8574 (tp) REVERT: S 111 ASP cc_start: 0.8472 (t0) cc_final: 0.7947 (t70) REVERT: L 91 MET cc_start: 0.8550 (mtm) cc_final: 0.7994 (mtm) REVERT: L 233 MET cc_start: 0.9403 (mmt) cc_final: 0.9183 (mmt) REVERT: L 296 LEU cc_start: 0.2049 (OUTLIER) cc_final: 0.0935 (tp) REVERT: Y 328 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8478 (ptpp) REVERT: Y 371 SER cc_start: 0.7089 (m) cc_final: 0.6822 (t) outliers start: 23 outliers final: 17 residues processed: 114 average time/residue: 0.2126 time to fit residues: 36.7385 Evaluate side-chains 116 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 171 ASP Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Chi-restraints excluded: chain Y residue 396 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11857 Z= 0.155 Angle : 0.567 12.587 16056 Z= 0.277 Chirality : 0.039 0.146 1807 Planarity : 0.004 0.052 2034 Dihedral : 4.232 28.613 1545 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.55 % Allowed : 16.60 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1392 helix: 1.25 (0.20), residues: 713 sheet: -1.69 (0.62), residues: 82 loop : -1.72 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 54 HIS 0.008 0.001 HIS P 48 PHE 0.024 0.001 PHE T 328 TYR 0.017 0.001 TYR L 180 ARG 0.007 0.000 ARG P 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8074 (tmm) cc_final: 0.7762 (tmm) REVERT: C 338 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7960 (ptmm) REVERT: K 14 ASP cc_start: 0.7428 (p0) cc_final: 0.6960 (p0) REVERT: S 110 LEU cc_start: 0.8904 (tp) cc_final: 0.8573 (tp) REVERT: S 111 ASP cc_start: 0.8384 (t0) cc_final: 0.7863 (t70) REVERT: L 91 MET cc_start: 0.8543 (mtm) cc_final: 0.8245 (mtm) REVERT: L 296 LEU cc_start: 0.2012 (OUTLIER) cc_final: 0.0905 (tp) REVERT: Y 328 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8472 (ptpp) REVERT: Y 371 SER cc_start: 0.7083 (m) cc_final: 0.6818 (t) outliers start: 20 outliers final: 17 residues processed: 115 average time/residue: 0.2245 time to fit residues: 38.5569 Evaluate side-chains 110 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 171 ASP Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Chi-restraints excluded: chain Y residue 396 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.7980 chunk 101 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 113 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 6 optimal weight: 0.0470 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.087470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067899 restraints weight = 41779.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070134 restraints weight = 22359.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.071591 restraints weight = 15121.555| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11857 Z= 0.141 Angle : 0.567 12.178 16056 Z= 0.275 Chirality : 0.039 0.208 1807 Planarity : 0.004 0.055 2034 Dihedral : 4.143 29.289 1545 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.24 % Allowed : 17.07 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1392 helix: 1.26 (0.20), residues: 714 sheet: -1.58 (0.62), residues: 82 loop : -1.64 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 54 HIS 0.004 0.001 HIS Y 296 PHE 0.024 0.001 PHE T 328 TYR 0.016 0.001 TYR L 180 ARG 0.005 0.000 ARG C 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2166.80 seconds wall clock time: 40 minutes 46.33 seconds (2446.33 seconds total)