Starting phenix.real_space_refine on Wed Feb 14 10:21:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqx_32095/02_2024/7vqx_32095_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqx_32095/02_2024/7vqx_32095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqx_32095/02_2024/7vqx_32095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqx_32095/02_2024/7vqx_32095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqx_32095/02_2024/7vqx_32095_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqx_32095/02_2024/7vqx_32095_neut.pdb" } resolution = 2.74 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= -0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5735 2.51 5 N 1566 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9049 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1962 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "L" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2877 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.30, per 1000 atoms: 0.59 Number of scatterers: 9049 At special positions: 0 Unit cell: (76.041, 101.745, 168.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1688 8.00 N 1566 7.00 C 5735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 38 " - pdb=" SG CYS R 61 " distance=2.04 Simple disulfide: pdb=" SG CYS R 52 " - pdb=" SG CYS R 93 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 271 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.9 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 41.8% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 4.657A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.500A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.568A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.748A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.936A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.714A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'L' and resid 2 through 27 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.740A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 43 removed outlier: 3.641A pdb=" N GLU R 30 " --> pdb=" O ARG R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 83 removed outlier: 5.183A pdb=" N ASN R 81 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 110 Processing helix chain 'R' and resid 115 through 117 No H-bonds generated for 'chain 'R' and resid 115 through 117' Processing helix chain 'R' and resid 118 through 151 removed outlier: 4.451A pdb=" N PHE R 122 " --> pdb=" O SER R 118 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR R 131 " --> pdb=" O LYS R 127 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR R 143 " --> pdb=" O MET R 139 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 156 through 184 Processing helix chain 'R' and resid 195 through 233 removed outlier: 4.282A pdb=" N TRP R 199 " --> pdb=" O GLN R 195 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 266 removed outlier: 4.245A pdb=" N LEU R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) Proline residue: R 252 - end of helix Processing helix chain 'R' and resid 277 through 312 removed outlier: 3.779A pdb=" N TRP R 281 " --> pdb=" O HIS R 277 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 3.508A pdb=" N SER R 312 " --> pdb=" O GLN R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 338 Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 341 through 347 removed outlier: 3.911A pdb=" N VAL R 346 " --> pdb=" O MET R 342 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE R 347 " --> pdb=" O VAL R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 365 removed outlier: 3.791A pdb=" N CYS R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 377 Processing helix chain 'R' and resid 379 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.365A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.382A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.629A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.545A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.874A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.576A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.872A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.574A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.009A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 70 through 74 451 hydrogen bonds defined for protein. 1302 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: 2.60 Time building geometry restraints manager: 3.62 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: 2955 1.34 - 1.46: 2043 1.46 - 1.58: 4162 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 9239 Sorted by residual: bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.01e+00 bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.47e-02 4.63e+03 1.71e+00 bond pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CB VAL N 110 " pdb=" CG1 VAL N 110 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB ARG A 232 " pdb=" CG ARG A 232 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 9234 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 192 106.37 - 113.27: 5018 113.27 - 120.18: 3255 120.18 - 127.09: 3945 127.09 - 134.00: 106 Bond angle restraints: 12516 Sorted by residual: angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.11 117.23 4.88 1.64e+00 3.72e-01 8.84e+00 angle pdb=" C ILE R 286 " pdb=" CA ILE R 286 " pdb=" CB ILE R 286 " ideal model delta sigma weight residual 114.00 110.95 3.05 1.31e+00 5.83e-01 5.41e+00 angle pdb=" N PHE N 108 " pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 110.80 115.67 -4.87 2.13e+00 2.20e-01 5.24e+00 angle pdb=" C ARG R 285 " pdb=" N ILE R 286 " pdb=" CA ILE R 286 " ideal model delta sigma weight residual 120.33 122.08 -1.75 8.00e-01 1.56e+00 4.80e+00 angle pdb=" N GLY B 216 " pdb=" CA GLY B 216 " pdb=" C GLY B 216 " ideal model delta sigma weight residual 113.18 118.16 -4.98 2.37e+00 1.78e-01 4.42e+00 ... (remaining 12511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4952 17.38 - 34.77: 455 34.77 - 52.15: 77 52.15 - 69.53: 12 69.53 - 86.91: 16 Dihedral angle restraints: 5512 sinusoidal: 2172 harmonic: 3340 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 169.30 -76.30 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS R 202 " pdb=" SG CYS R 202 " pdb=" SG CYS R 271 " pdb=" CB CYS R 271 " ideal model delta sinusoidal sigma weight residual 93.00 155.70 -62.70 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS R 38 " pdb=" SG CYS R 38 " pdb=" SG CYS R 61 " pdb=" CB CYS R 61 " ideal model delta sinusoidal sigma weight residual 93.00 137.10 -44.10 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 5509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 797 0.029 - 0.058: 384 0.058 - 0.087: 146 0.087 - 0.116: 61 0.116 - 0.145: 16 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1401 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO B 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 138 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C LEU R 138 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU R 138 " 0.012 2.00e-02 2.50e+03 pdb=" N MET R 139 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 131 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C THR R 131 " -0.032 2.00e-02 2.50e+03 pdb=" O THR R 131 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU R 132 " 0.011 2.00e-02 2.50e+03 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 125 2.66 - 3.22: 8325 3.22 - 3.78: 14306 3.78 - 4.34: 19806 4.34 - 4.90: 32728 Nonbonded interactions: 75290 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.094 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.147 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.172 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.238 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.259 2.520 ... (remaining 75285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.120 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 27.750 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.004 0.047 9239 Z= 0.233 Angle : 0.547 6.898 12516 Z= 0.298 Chirality : 0.042 0.145 1404 Planarity : 0.004 0.053 1594 Dihedral : 14.120 86.912 3334 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1130 helix: 1.55 (0.25), residues: 428 sheet: -0.19 (0.32), residues: 244 loop : -0.81 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 219 HIS 0.012 0.001 HIS A 357 PHE 0.018 0.001 PHE B 234 TYR 0.017 0.002 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8197 (mt) cc_final: 0.7967 (mt) REVERT: A 299 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 170 ASP cc_start: 0.7488 (t70) cc_final: 0.7106 (t70) REVERT: B 175 GLN cc_start: 0.7673 (mm110) cc_final: 0.7331 (mp10) REVERT: R 34 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6507 (tm-30) REVERT: R 354 LYS cc_start: 0.6914 (mttp) cc_final: 0.6365 (ptmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 1.4419 time to fit residues: 166.6999 Evaluate side-chains 94 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9239 Z= 0.266 Angle : 0.546 6.714 12516 Z= 0.291 Chirality : 0.042 0.143 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.376 17.637 1247 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.12 % Allowed : 7.92 % Favored : 90.96 % 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: 0.64 (0.25), residues: 1130 helix: 1.98 (0.25), residues: 443 sheet: -0.12 (0.32), residues: 249 loop : -0.84 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 219 HIS 0.011 0.001 HIS A 357 PHE 0.016 0.001 PHE B 234 TYR 0.034 0.002 TYR R 130 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.053 Fit side-chains REVERT: A 296 LEU cc_start: 0.8123 (mt) cc_final: 0.7882 (mt) REVERT: A 392 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: B 175 GLN cc_start: 0.7665 (mm110) cc_final: 0.7336 (mp10) REVERT: R 34 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6508 (tm-30) REVERT: R 354 LYS cc_start: 0.6937 (mttp) cc_final: 0.6469 (ptmm) outliers start: 11 outliers final: 9 residues processed: 111 average time/residue: 1.3804 time to fit residues: 162.9075 Evaluate side-chains 111 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.0370 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9239 Z= 0.223 Angle : 0.508 6.625 12516 Z= 0.271 Chirality : 0.041 0.140 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.242 16.954 1247 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.44 % Allowed : 9.64 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1130 helix: 2.16 (0.25), residues: 443 sheet: -0.07 (0.32), residues: 249 loop : -0.84 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 219 HIS 0.009 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.025 0.001 TYR R 130 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.138 Fit side-chains REVERT: A 296 LEU cc_start: 0.8215 (mt) cc_final: 0.7981 (mt) REVERT: A 392 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: B 170 ASP cc_start: 0.7502 (t70) cc_final: 0.7123 (t70) REVERT: B 175 GLN cc_start: 0.7665 (mm110) cc_final: 0.7318 (mp10) REVERT: N 65 LYS cc_start: 0.7452 (ptpp) cc_final: 0.7249 (ttmt) REVERT: R 354 LYS cc_start: 0.6947 (mttp) cc_final: 0.6457 (ptmm) outliers start: 24 outliers final: 12 residues processed: 109 average time/residue: 1.3268 time to fit residues: 154.3149 Evaluate side-chains 105 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9239 Z= 0.198 Angle : 0.493 6.452 12516 Z= 0.263 Chirality : 0.041 0.137 1404 Planarity : 0.003 0.051 1594 Dihedral : 4.169 18.286 1247 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.03 % Allowed : 12.59 % Favored : 85.38 % 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: 0.89 (0.26), residues: 1130 helix: 2.34 (0.25), residues: 440 sheet: -0.09 (0.32), residues: 249 loop : -0.80 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 219 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.024 0.001 TYR R 130 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.052 Fit side-chains REVERT: A 296 LEU cc_start: 0.8165 (mt) cc_final: 0.7912 (mt) REVERT: A 299 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6484 (mm-30) REVERT: A 392 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: B 175 GLN cc_start: 0.7656 (mm110) cc_final: 0.7317 (mp10) REVERT: B 217 MET cc_start: 0.7474 (pp-130) cc_final: 0.7185 (ppp) REVERT: R 185 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7710 (p) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 1.4455 time to fit residues: 169.5762 Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 0.0010 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9239 Z= 0.189 Angle : 0.484 6.662 12516 Z= 0.258 Chirality : 0.040 0.138 1404 Planarity : 0.003 0.050 1594 Dihedral : 4.082 16.336 1247 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.64 % Allowed : 13.40 % Favored : 83.96 % 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: 0.96 (0.26), residues: 1130 helix: 2.42 (0.25), residues: 440 sheet: -0.09 (0.32), residues: 249 loop : -0.75 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.023 0.001 TYR R 130 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.089 Fit side-chains REVERT: A 296 LEU cc_start: 0.8109 (mt) cc_final: 0.7884 (mt) REVERT: A 299 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 392 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: B 175 GLN cc_start: 0.7647 (mm110) cc_final: 0.7309 (mp10) REVERT: B 217 MET cc_start: 0.7473 (pp-130) cc_final: 0.7236 (ppp) REVERT: R 35 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7133 (mp0) REVERT: R 185 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7681 (p) REVERT: R 381 GLU cc_start: 0.7406 (tt0) cc_final: 0.7185 (pt0) outliers start: 26 outliers final: 15 residues processed: 112 average time/residue: 1.2014 time to fit residues: 144.1045 Evaluate side-chains 113 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9239 Z= 0.189 Angle : 0.482 7.032 12516 Z= 0.258 Chirality : 0.040 0.136 1404 Planarity : 0.003 0.050 1594 Dihedral : 4.044 16.099 1247 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.94 % Allowed : 13.40 % Favored : 83.65 % 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: 0.99 (0.26), residues: 1130 helix: 2.44 (0.25), residues: 440 sheet: -0.07 (0.32), residues: 249 loop : -0.74 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.022 0.001 TYR R 130 ARG 0.001 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.973 Fit side-chains REVERT: A 296 LEU cc_start: 0.8143 (mt) cc_final: 0.7920 (mt) REVERT: A 299 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6513 (mm-30) REVERT: A 392 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 175 GLN cc_start: 0.7644 (mm110) cc_final: 0.7302 (mp10) REVERT: B 217 MET cc_start: 0.7424 (pp-130) cc_final: 0.7062 (ppp) REVERT: G 21 MET cc_start: 0.6183 (mmm) cc_final: 0.5403 (ttt) REVERT: R 35 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7230 (mp0) REVERT: R 185 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7669 (p) REVERT: R 267 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: R 381 GLU cc_start: 0.7410 (tt0) cc_final: 0.7198 (pt0) outliers start: 29 outliers final: 17 residues processed: 114 average time/residue: 1.2598 time to fit residues: 153.3958 Evaluate side-chains 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 79 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9239 Z= 0.184 Angle : 0.480 7.475 12516 Z= 0.258 Chirality : 0.040 0.136 1404 Planarity : 0.003 0.052 1594 Dihedral : 4.066 21.374 1247 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.54 % Allowed : 14.62 % Favored : 82.84 % 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: 1.04 (0.26), residues: 1130 helix: 2.50 (0.25), residues: 440 sheet: -0.02 (0.33), residues: 249 loop : -0.75 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.022 0.001 TYR R 130 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.071 Fit side-chains REVERT: A 296 LEU cc_start: 0.8170 (mt) cc_final: 0.7948 (mt) REVERT: A 299 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6508 (mm-30) REVERT: A 392 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: B 175 GLN cc_start: 0.7641 (mm110) cc_final: 0.7298 (mp10) REVERT: R 35 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7354 (mp0) REVERT: R 185 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7655 (p) REVERT: R 267 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: R 381 GLU cc_start: 0.7416 (tt0) cc_final: 0.7211 (pt0) outliers start: 25 outliers final: 16 residues processed: 110 average time/residue: 1.3160 time to fit residues: 154.6243 Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.0010 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9239 Z= 0.162 Angle : 0.475 7.018 12516 Z= 0.254 Chirality : 0.040 0.143 1404 Planarity : 0.003 0.054 1594 Dihedral : 3.986 21.133 1247 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.23 % Allowed : 15.43 % Favored : 82.34 % 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: 1.08 (0.26), residues: 1130 helix: 2.53 (0.25), residues: 441 sheet: 0.06 (0.33), residues: 247 loop : -0.77 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 219 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR R 130 ARG 0.001 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.101 Fit side-chains REVERT: A 296 LEU cc_start: 0.8137 (mt) cc_final: 0.7913 (mt) REVERT: A 299 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6494 (mm-30) REVERT: B 175 GLN cc_start: 0.7673 (mm110) cc_final: 0.7337 (mp10) REVERT: R 35 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7271 (mp0) REVERT: R 185 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7634 (p) REVERT: R 267 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: R 354 LYS cc_start: 0.7191 (mttt) cc_final: 0.6565 (ptmm) outliers start: 22 outliers final: 15 residues processed: 110 average time/residue: 1.3140 time to fit residues: 155.2470 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 378 LEU Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9239 Z= 0.182 Angle : 0.490 7.312 12516 Z= 0.259 Chirality : 0.040 0.136 1404 Planarity : 0.003 0.054 1594 Dihedral : 4.002 19.894 1247 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.73 % Allowed : 16.55 % Favored : 81.73 % 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: 1.12 (0.26), residues: 1130 helix: 2.57 (0.25), residues: 441 sheet: 0.06 (0.33), residues: 247 loop : -0.75 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.022 0.001 TYR R 130 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.067 Fit side-chains REVERT: A 296 LEU cc_start: 0.8150 (mt) cc_final: 0.7926 (mt) REVERT: A 299 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6490 (mm-30) REVERT: B 175 GLN cc_start: 0.7637 (mm110) cc_final: 0.7296 (mp10) REVERT: R 35 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7312 (mp0) REVERT: R 185 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7633 (p) REVERT: R 267 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7315 (pt0) REVERT: R 354 LYS cc_start: 0.7197 (mttt) cc_final: 0.6569 (ptmm) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 1.2521 time to fit residues: 138.0938 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 378 LEU Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9239 Z= 0.148 Angle : 0.477 8.778 12516 Z= 0.251 Chirality : 0.039 0.134 1404 Planarity : 0.003 0.054 1594 Dihedral : 3.902 19.770 1247 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.73 % Allowed : 16.45 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1130 helix: 2.53 (0.25), residues: 447 sheet: 0.11 (0.33), residues: 245 loop : -0.79 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 219 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.020 0.001 TYR R 130 ARG 0.003 0.000 ARG R 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.027 Fit side-chains REVERT: A 296 LEU cc_start: 0.8185 (mt) cc_final: 0.7966 (mt) REVERT: A 299 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6498 (mm-30) REVERT: B 175 GLN cc_start: 0.7680 (mm110) cc_final: 0.7348 (mp10) REVERT: B 186 ASP cc_start: 0.6597 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: N 35 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7416 (p0) REVERT: R 34 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6666 (tm-30) REVERT: R 35 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7394 (mm-30) REVERT: R 185 SER cc_start: 0.7887 (OUTLIER) cc_final: 0.7612 (p) REVERT: R 267 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: R 354 LYS cc_start: 0.7183 (mttt) cc_final: 0.6561 (ptmm) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 1.2073 time to fit residues: 141.0588 Evaluate side-chains 111 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.0060 chunk 5 optimal weight: 5.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.182976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123116 restraints weight = 8924.872| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.02 r_work: 0.3036 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9239 Z= 0.349 Angle : 0.592 9.150 12516 Z= 0.310 Chirality : 0.044 0.153 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.308 19.372 1247 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.83 % Allowed : 16.65 % Favored : 81.52 % 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: 0.88 (0.26), residues: 1130 helix: 2.32 (0.25), residues: 445 sheet: -0.04 (0.32), residues: 251 loop : -0.88 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 219 HIS 0.011 0.001 HIS A 357 PHE 0.014 0.002 PHE B 151 TYR 0.029 0.002 TYR R 130 ARG 0.005 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3465.07 seconds wall clock time: 62 minutes 33.82 seconds (3753.82 seconds total)